Starting phenix.real_space_refine on Sat Mar 7 15:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.map" model { file = "/net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x89_22090/03_2026/6x89_22090.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 2 6.06 5 P 10 5.49 5 S 297 5.16 5 C 28847 2.51 5 N 7646 2.21 5 O 8187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45017 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A2" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "A5" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "A6" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 129 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A7" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 96} Chain: "A9" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2548 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 22, 'TRANS': 305} Chain breaks: 1 Chain: "AL" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1128 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "S1" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5268 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 650} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "S2" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3044 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 19, 'TRANS': 362} Chain breaks: 1 Chain: "S3" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1559 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S4" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S6" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 563 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 7, 'TRANS': 64} Chain: "S7" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 147} Chain: "S8" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1484 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "V1" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3343 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain: "V2" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1M" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2463 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 298} Chain breaks: 1 Chain: "2M" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3795 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 469} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "3M" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "4L" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "6M" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1142 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "A1" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "A3" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 332 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A8" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "AM" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1134 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 13, 'TRANS': 128} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "C2" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P2" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 214 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S5" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 560 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "X1" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 750 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "G1" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1769 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "G2" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1799 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 230} Chain: "L2" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1611 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S2" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C2" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "G1" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' ZN': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7354 SG CYSS1 171 67.850 128.575 66.071 1.00 39.66 S ATOM 7415 SG CYSS1 180 65.172 126.543 59.635 1.00 40.31 S ATOM 7375 SG CYSS1 174 61.493 128.055 65.666 1.00 42.33 S ATOM 7719 SG CYSS1 219 56.270 136.094 58.045 1.00 55.13 S ATOM 8088 SG CYSS1 269 56.296 129.335 57.923 1.00 38.45 S ATOM 7742 SG CYSS1 222 57.883 132.529 52.540 1.00 36.30 S ATOM 6871 SG CYSS1 107 62.215 132.983 46.764 1.00 45.54 S ATOM 6955 SG CYSS1 118 65.632 132.374 48.194 1.00 40.78 S ATOM 6980 SG CYSS1 121 67.570 130.957 42.990 1.00 45.15 S ATOM 7082 SG CYSS1 135 63.831 131.499 41.726 1.00 50.36 S ATOM 17445 SG CYSS6 65 64.508 137.682 80.463 1.00 62.07 S ATOM 17629 SG CYSS6 90 62.521 136.700 78.186 1.00 54.84 S ATOM 17656 SG CYSS6 93 64.236 134.811 81.972 1.00 59.53 S ATOM 19980 SG CYSS8 162 74.362 110.510 84.070 1.00 46.84 S ATOM 20027 SG CYSS8 168 73.316 115.738 81.256 1.00 45.41 S ATOM 20006 SG CYSS8 165 79.187 112.745 79.076 1.00 39.34 S ATOM 19748 SG CYSS8 133 72.593 110.183 77.911 1.00 32.83 S ATOM 19678 SG CYSS8 123 64.107 121.302 80.757 1.00 38.85 S ATOM 19720 SG CYSS8 129 68.630 116.873 78.344 1.00 36.71 S ATOM 19697 SG CYSS8 126 66.826 123.441 75.147 1.00 34.11 S ATOM 20056 SG CYSS8 172 70.684 123.670 79.730 1.00 41.52 S ATOM 23185 SG CYSV1 413 66.107 145.645 49.999 1.00 49.32 S ATOM 24610 SG CYSV2 126 62.375 167.250 53.065 1.00 74.98 S ATOM 24641 SG CYSV2 131 64.318 170.529 52.997 1.00 78.51 S ATOM 24912 SG CYSV2 167 63.572 165.381 48.399 1.00 70.23 S ATOM 24936 SG CYSV2 171 65.670 168.062 47.114 1.00 74.53 S Time building chain proxies: 9.31, per 1000 atoms: 0.21 Number of scatterers: 45017 At special positions: 0 Unit cell: (184.137, 197.468, 179.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 28 26.01 S 297 16.00 P 10 15.00 O 8187 8.00 N 7646 7.00 C 28847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS2M 325 " - pdb=" SG CYS2M 409 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 29 " - pdb=" SG CYSA8 59 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 39 " - pdb=" SG CYSA8 49 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 71 " - pdb=" SG CYSA8 103 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 81 " - pdb=" SG CYSA8 92 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 14 " - pdb=" SG CYSS5 44 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 24 " - pdb=" SG CYSS5 34 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 118 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 107 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 135 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 121 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 167 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 126 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 171 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 131 " pdb=" SF4S1 801 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 171 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 174 " pdb="FE2 SF4S1 801 " - pdb=" NE2 HISS1 167 " pdb="FE3 SF4S1 801 " - pdb=" SG CYSS1 180 " pdb=" SF4S1 802 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 222 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 219 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 269 " pdb=" SF4S7 301 " pdb="FE4 SF4S7 301 " - pdb=" SG CYSS7 88 " pdb=" SF4S8 301 " pdb="FE2 SF4S8 301 " - pdb=" SG CYSS8 168 " pdb="FE1 SF4S8 301 " - pdb=" SG CYSS8 162 " pdb="FE4 SF4S8 301 " - pdb=" SG CYSS8 133 " pdb="FE3 SF4S8 301 " - pdb=" SG CYSS8 165 " pdb=" SF4S8 302 " pdb="FE4 SF4S8 302 " - pdb=" SG CYSS8 172 " pdb="FE3 SF4S8 302 " - pdb=" SG CYSS8 126 " pdb="FE2 SF4S8 302 " - pdb=" SG CYSS8 129 " pdb="FE1 SF4S8 302 " - pdb=" SG CYSS8 123 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 413 " Number of angles added : 60 Zn2+ tetrahedral coordination pdb=" ZNG1 703 " pdb="ZN ZNG1 703 " - pdb=" NE2 HISG2 135 " pdb="ZN ZNG1 703 " - pdb=" NE2 HISG1 130 " pdb="ZN ZNG1 703 " - pdb=" ND1 HISG2 107 " pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 75 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 65 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 90 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 93 " Number of angles added : 3 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10604 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 37 sheets defined 52.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A2' and resid 27 through 43 Processing helix chain 'A2' and resid 78 through 91 Processing helix chain 'A5' and resid 28 through 47 Processing helix chain 'A5' and resid 51 through 72 Processing helix chain 'A5' and resid 73 through 82 Processing helix chain 'A5' and resid 85 through 106 Processing helix chain 'A6' and resid 121 through 128 removed outlier: 3.762A pdb=" N SERA6 128 " --> pdb=" O LYSA6 124 " (cutoff:3.500A) Processing helix chain 'A7' and resid 25 through 29 removed outlier: 3.627A pdb=" N ASPA7 29 " --> pdb=" O PROA7 26 " (cutoff:3.500A) Processing helix chain 'A7' and resid 38 through 43 Processing helix chain 'A7' and resid 60 through 66 Processing helix chain 'A7' and resid 68 through 73 Processing helix chain 'A7' and resid 87 through 98 Processing helix chain 'A7' and resid 120 through 126 removed outlier: 3.755A pdb=" N GLNA7 126 " --> pdb=" O GLYA7 122 " (cutoff:3.500A) Processing helix chain 'A9' and resid 72 through 86 Processing helix chain 'A9' and resid 101 through 105 Processing helix chain 'A9' and resid 121 through 129 Processing helix chain 'A9' and resid 149 through 168 Processing helix chain 'A9' and resid 189 through 205 Processing helix chain 'A9' and resid 223 through 234 Processing helix chain 'A9' and resid 252 through 265 Processing helix chain 'A9' and resid 284 through 296 Processing helix chain 'A9' and resid 304 through 322 removed outlier: 4.063A pdb=" N ILEA9 308 " --> pdb=" O VALA9 304 " (cutoff:3.500A) Proline residue: A9 315 - end of helix removed outlier: 3.704A pdb=" N ILEA9 318 " --> pdb=" O THRA9 314 " (cutoff:3.500A) Processing helix chain 'A9' and resid 334 through 343 Processing helix chain 'A9' and resid 353 through 358 Processing helix chain 'A9' and resid 369 through 375 removed outlier: 3.711A pdb=" N SERA9 374 " --> pdb=" O PHEA9 371 " (cutoff:3.500A) Processing helix chain 'AL' and resid 22 through 29 Processing helix chain 'AL' and resid 31 through 36 Processing helix chain 'AL' and resid 36 through 47 Processing helix chain 'AL' and resid 89 through 98 Processing helix chain 'AL' and resid 103 through 111 Processing helix chain 'AL' and resid 126 through 131 removed outlier: 4.142A pdb=" N TYRAL 130 " --> pdb=" O GLUAL 126 " (cutoff:3.500A) Processing helix chain 'S1' and resid 91 through 100 Processing helix chain 'S1' and resid 149 through 166 Processing helix chain 'S1' and resid 180 through 190 Processing helix chain 'S1' and resid 216 through 219 Processing helix chain 'S1' and resid 223 through 232 Processing helix chain 'S1' and resid 261 through 269 Processing helix chain 'S1' and resid 278 through 280 No H-bonds generated for 'chain 'S1' and resid 278 through 280' Processing helix chain 'S1' and resid 330 through 335 removed outlier: 3.642A pdb=" N ARGS1 334 " --> pdb=" O SERS1 330 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHES1 335 " --> pdb=" O ASPS1 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 330 through 335' Processing helix chain 'S1' and resid 337 through 343 Processing helix chain 'S1' and resid 361 through 376 Processing helix chain 'S1' and resid 390 through 405 Processing helix chain 'S1' and resid 422 through 427 Processing helix chain 'S1' and resid 432 through 438 removed outlier: 3.582A pdb=" N ALAS1 438 " --> pdb=" O LEUS1 435 " (cutoff:3.500A) Processing helix chain 'S1' and resid 452 through 466 Processing helix chain 'S1' and resid 489 through 498 Processing helix chain 'S1' and resid 502 through 509 removed outlier: 3.752A pdb=" N THRS1 506 " --> pdb=" O PROS1 502 " (cutoff:3.500A) Processing helix chain 'S1' and resid 519 through 524 removed outlier: 3.564A pdb=" N GLUS1 523 " --> pdb=" O GLYS1 520 " (cutoff:3.500A) Processing helix chain 'S1' and resid 527 through 542 Processing helix chain 'S1' and resid 559 through 567 Processing helix chain 'S1' and resid 574 through 579 Processing helix chain 'S1' and resid 588 through 594 removed outlier: 3.614A pdb=" N LYSS1 594 " --> pdb=" O VALS1 590 " (cutoff:3.500A) Processing helix chain 'S1' and resid 611 through 615 Processing helix chain 'S1' and resid 653 through 665 Processing helix chain 'S1' and resid 673 through 685 Processing helix chain 'S1' and resid 686 through 690 Processing helix chain 'S1' and resid 727 through 733 Processing helix chain 'S1' and resid 734 through 743 Processing helix chain 'S2' and resid 50 through 57 Processing helix chain 'S2' and resid 63 through 70 removed outlier: 3.687A pdb=" N PHES2 67 " --> pdb=" O ALAS2 63 " (cutoff:3.500A) Processing helix chain 'S2' and resid 76 through 91 Processing helix chain 'S2' and resid 95 through 126 Processing helix chain 'S2' and resid 128 through 149 Processing helix chain 'S2' and resid 170 through 194 Processing helix chain 'S2' and resid 196 through 204 Processing helix chain 'S2' and resid 210 through 217 Processing helix chain 'S2' and resid 220 through 226 Processing helix chain 'S2' and resid 232 through 237 Processing helix chain 'S2' and resid 240 through 244 removed outlier: 3.988A pdb=" N ASPS2 243 " --> pdb=" O ASPS2 240 " (cutoff:3.500A) Processing helix chain 'S2' and resid 256 through 282 Proline residue: S2 279 - end of helix Processing helix chain 'S2' and resid 298 through 305 Processing helix chain 'S2' and resid 306 through 318 Processing helix chain 'S2' and resid 358 through 370 Processing helix chain 'S2' and resid 374 through 386 Processing helix chain 'S2' and resid 388 through 394 Processing helix chain 'S3' and resid 3 through 14 Processing helix chain 'S3' and resid 15 through 19 removed outlier: 3.505A pdb=" N TRPS3 18 " --> pdb=" O PROS3 15 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VALS3 19 " --> pdb=" O LYSS3 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'S3' and resid 15 through 19' Processing helix chain 'S3' and resid 37 through 45 Processing helix chain 'S3' and resid 108 through 118 Processing helix chain 'S4' and resid 91 through 95 Processing helix chain 'S4' and resid 101 through 113 Processing helix chain 'S4' and resid 130 through 135 Processing helix chain 'S6' and resid 32 through 38 Processing helix chain 'S6' and resid 45 through 53 Processing helix chain 'S7' and resid 57 through 78 Processing helix chain 'S7' and resid 88 through 98 Processing helix chain 'S7' and resid 103 through 107 Processing helix chain 'S7' and resid 130 through 140 removed outlier: 3.582A pdb=" N GLNS7 140 " --> pdb=" O LYSS7 136 " (cutoff:3.500A) Processing helix chain 'S7' and resid 159 through 163 Processing helix chain 'S7' and resid 169 through 173 Processing helix chain 'S7' and resid 186 through 203 removed outlier: 3.759A pdb=" N ARGS7 203 " --> pdb=" O LYSS7 199 " (cutoff:3.500A) Processing helix chain 'S7' and resid 206 through 213 Processing helix chain 'S8' and resid 43 through 57 removed outlier: 3.665A pdb=" N ILES8 56 " --> pdb=" O LEUS8 52 " (cutoff:3.500A) Processing helix chain 'S8' and resid 59 through 73 removed outlier: 3.713A pdb=" N VALS8 63 " --> pdb=" O ASPS8 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEUS8 73 " --> pdb=" O ASNS8 69 " (cutoff:3.500A) Processing helix chain 'S8' and resid 73 through 89 Processing helix chain 'S8' and resid 95 through 99 Processing helix chain 'S8' and resid 127 through 133 Processing helix chain 'S8' and resid 167 through 172 Processing helix chain 'S8' and resid 198 through 203 Processing helix chain 'S8' and resid 204 through 206 No H-bonds generated for 'chain 'S8' and resid 204 through 206' Processing helix chain 'S8' and resid 207 through 220 removed outlier: 4.227A pdb=" N LEUS8 220 " --> pdb=" O ARGS8 216 " (cutoff:3.500A) Processing helix chain 'V1' and resid 92 through 99 Processing helix chain 'V1' and resid 100 through 112 removed outlier: 3.622A pdb=" N ILEV1 104 " --> pdb=" O GLYV1 100 " (cutoff:3.500A) Processing helix chain 'V1' and resid 122 through 129 Processing helix chain 'V1' and resid 154 through 162 Processing helix chain 'V1' and resid 162 through 177 removed outlier: 4.125A pdb=" N LEUV1 166 " --> pdb=" O ASPV1 162 " (cutoff:3.500A) Processing helix chain 'V1' and resid 190 through 207 Processing helix chain 'V1' and resid 232 through 235 Processing helix chain 'V1' and resid 236 through 246 Processing helix chain 'V1' and resid 273 through 285 Proline residue: V1 280 - end of helix Processing helix chain 'V1' and resid 286 through 292 removed outlier: 3.753A pdb=" N PHEV1 290 " --> pdb=" O GLYV1 286 " (cutoff:3.500A) Processing helix chain 'V1' and resid 323 through 331 Processing helix chain 'V1' and resid 368 through 374 Processing helix chain 'V1' and resid 390 through 404 Processing helix chain 'V1' and resid 410 through 430 removed outlier: 3.907A pdb=" N ARGV1 414 " --> pdb=" O CYSV1 410 " (cutoff:3.500A) Processing helix chain 'V1' and resid 433 through 450 removed outlier: 3.669A pdb=" N ILEV1 437 " --> pdb=" O LYSV1 433 " (cutoff:3.500A) Processing helix chain 'V1' and resid 454 through 470 Proline residue: V1 462 - end of helix Processing helix chain 'V1' and resid 470 through 490 removed outlier: 3.533A pdb=" N LEUV1 474 " --> pdb=" O PHEV1 470 " (cutoff:3.500A) Processing helix chain 'V2' and resid 46 through 58 Processing helix chain 'V2' and resid 65 through 67 No H-bonds generated for 'chain 'V2' and resid 65 through 67' Processing helix chain 'V2' and resid 68 through 80 removed outlier: 3.522A pdb=" N ASPV2 74 " --> pdb=" O ILEV2 70 " (cutoff:3.500A) Processing helix chain 'V2' and resid 85 through 96 Processing helix chain 'V2' and resid 99 through 110 removed outlier: 4.195A pdb=" N VALV2 103 " --> pdb=" O PROV2 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYRV2 110 " --> pdb=" O VALV2 106 " (cutoff:3.500A) Processing helix chain 'V2' and resid 128 through 133 Processing helix chain 'V2' and resid 135 through 147 removed outlier: 4.069A pdb=" N ILEV2 139 " --> pdb=" O GLYV2 135 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEUV2 147 " --> pdb=" O LEUV2 143 " (cutoff:3.500A) Processing helix chain 'V2' and resid 198 through 211 Processing helix chain '1M' and resid 3 through 35 Proline residue: 1M 15 - end of helix Processing helix chain '1M' and resid 49 through 61 Processing helix chain '1M' and resid 76 through 90 Processing helix chain '1M' and resid 105 through 127 Processing helix chain '1M' and resid 131 through 161 Processing helix chain '1M' and resid 166 through 177 removed outlier: 3.861A pdb=" N ILE1M 177 " --> pdb=" O ALA1M 173 " (cutoff:3.500A) Processing helix chain '1M' and resid 183 through 198 removed outlier: 3.511A pdb=" N THR1M 198 " --> pdb=" O CYS1M 194 " (cutoff:3.500A) Processing helix chain '1M' and resid 204 through 211 Processing helix chain '1M' and resid 221 through 247 Processing helix chain '1M' and resid 259 through 263 Processing helix chain '1M' and resid 265 through 285 Processing helix chain '1M' and resid 292 through 302 Processing helix chain '1M' and resid 302 through 321 removed outlier: 3.717A pdb=" N LEU1M 306 " --> pdb=" O VAL1M 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE1M 321 " --> pdb=" O VAL1M 317 " (cutoff:3.500A) Processing helix chain '2M' and resid 4 through 7 Processing helix chain '2M' and resid 8 through 30 Processing helix chain '2M' and resid 39 through 66 Proline residue: 2M 63 - end of helix Processing helix chain '2M' and resid 68 through 74 Processing helix chain '2M' and resid 79 through 108 removed outlier: 4.945A pdb=" N ASP2M 102 " --> pdb=" O SER2M 98 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE2M 103 " --> pdb=" O MET2M 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE2M 104 " --> pdb=" O CYS2M 100 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU2M 105 " --> pdb=" O PHE2M 101 " (cutoff:3.500A) Processing helix chain '2M' and resid 112 through 130 removed outlier: 3.703A pdb=" N ILE2M 118 " --> pdb=" O PHE2M 114 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU2M 119 " --> pdb=" O ILE2M 115 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU2M 120 " --> pdb=" O VAL2M 116 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER2M 130 " --> pdb=" O LEU2M 126 " (cutoff:3.500A) Processing helix chain '2M' and resid 133 through 153 removed outlier: 4.080A pdb=" N ALA2M 153 " --> pdb=" O TYR2M 149 " (cutoff:3.500A) Processing helix chain '2M' and resid 159 through 191 removed outlier: 4.087A pdb=" N GLU2M 163 " --> pdb=" O GLU2M 159 " (cutoff:3.500A) Processing helix chain '2M' and resid 194 through 203 Processing helix chain '2M' and resid 209 through 211 No H-bonds generated for 'chain '2M' and resid 209 through 211' Processing helix chain '2M' and resid 212 through 229 removed outlier: 3.967A pdb=" N PHE2M 216 " --> pdb=" O SER2M 212 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET2M 217 " --> pdb=" O SER2M 213 " (cutoff:3.500A) Processing helix chain '2M' and resid 230 through 231 No H-bonds generated for 'chain '2M' and resid 230 through 231' Processing helix chain '2M' and resid 232 through 236 removed outlier: 3.656A pdb=" N HIS2M 236 " --> pdb=" O VAL2M 233 " (cutoff:3.500A) Processing helix chain '2M' and resid 238 through 246 Processing helix chain '2M' and resid 247 through 273 Proline residue: 2M 258 - end of helix removed outlier: 3.834A pdb=" N TYR2M 272 " --> pdb=" O ARG2M 268 " (cutoff:3.500A) Processing helix chain '2M' and resid 277 through 299 removed outlier: 4.085A pdb=" N CYS2M 286 " --> pdb=" O ILE2M 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE2M 288 " --> pdb=" O CYS2M 284 " (cutoff:3.500A) Processing helix chain '2M' and resid 303 through 323 removed outlier: 3.803A pdb=" N LEU2M 308 " --> pdb=" O VAL2M 304 " (cutoff:3.500A) Processing helix chain '2M' and resid 327 through 355 Processing helix chain '2M' and resid 356 through 360 Processing helix chain '2M' and resid 368 through 373 Processing helix chain '2M' and resid 373 through 389 Processing helix chain '2M' and resid 393 through 409 removed outlier: 3.534A pdb=" N CYS2M 397 " --> pdb=" O LEU2M 393 " (cutoff:3.500A) Processing helix chain '2M' and resid 413 through 434 removed outlier: 3.997A pdb=" N VAL2M 417 " --> pdb=" O PHE2M 413 " (cutoff:3.500A) Processing helix chain '2M' and resid 435 through 437 No H-bonds generated for 'chain '2M' and resid 435 through 437' Processing helix chain '2M' and resid 452 through 467 removed outlier: 3.597A pdb=" N THR2M 466 " --> pdb=" O SER2M 462 " (cutoff:3.500A) Processing helix chain '2M' and resid 472 through 488 removed outlier: 3.994A pdb=" N PHE2M 476 " --> pdb=" O PRO2M 472 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR2M 487 " --> pdb=" O ALA2M 483 " (cutoff:3.500A) Processing helix chain '3M' and resid 3 through 24 Processing helix chain '3M' and resid 58 through 83 Proline residue: 3M 72 - end of helix Proline residue: 3M 79 - end of helix Processing helix chain '3M' and resid 88 through 113 removed outlier: 3.903A pdb=" N SER3M 92 " --> pdb=" O ASP3M 88 " (cutoff:3.500A) Processing helix chain '4L' and resid 2 through 24 Processing helix chain '4L' and resid 27 through 53 Processing helix chain '4L' and resid 56 through 84 removed outlier: 3.705A pdb=" N SER4L 60 " --> pdb=" O MET4L 56 " (cutoff:3.500A) Processing helix chain '6M' and resid 2 through 20 Processing helix chain '6M' and resid 22 through 45 removed outlier: 3.665A pdb=" N SER6M 26 " --> pdb=" O ASN6M 22 " (cutoff:3.500A) Processing helix chain '6M' and resid 46 through 56 removed outlier: 3.667A pdb=" N ALA6M 50 " --> pdb=" O LEU6M 46 " (cutoff:3.500A) Processing helix chain '6M' and resid 60 through 72 removed outlier: 3.527A pdb=" N LEU6M 64 " --> pdb=" O ALA6M 60 " (cutoff:3.500A) Processing helix chain '6M' and resid 98 through 106 Processing helix chain '6M' and resid 112 through 119 removed outlier: 3.520A pdb=" N GLN6M 116 " --> pdb=" O LEU6M 112 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN6M 118 " --> pdb=" O PRO6M 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR6M 119 " --> pdb=" O THR6M 115 " (cutoff:3.500A) Processing helix chain '6M' and resid 120 through 123 removed outlier: 4.309A pdb=" N ILE6M 123 " --> pdb=" O THR6M 120 " (cutoff:3.500A) No H-bonds generated for 'chain '6M' and resid 120 through 123' Processing helix chain '6M' and resid 135 through 147 Processing helix chain '6M' and resid 149 through 171 Proline residue: 6M 155 - end of helix Processing helix chain 'A1' and resid 5 through 35 removed outlier: 3.594A pdb=" N VALA1 9 " --> pdb=" O TRPA1 5 " (cutoff:3.500A) Proline residue: A1 11 - end of helix removed outlier: 3.615A pdb=" N ILEA1 15 " --> pdb=" O PROA1 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLNA1 26 " --> pdb=" O META1 22 " (cutoff:3.500A) Processing helix chain 'A1' and resid 43 through 63 Processing helix chain 'A3' and resid 3 through 14 Processing helix chain 'A3' and resid 14 through 45 Proline residue: A3 31 - end of helix Proline residue: A3 36 - end of helix Processing helix chain 'A8' and resid 15 through 26 removed outlier: 4.558A pdb=" N HISA8 24 " --> pdb=" O ALAA8 20 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLYA8 26 " --> pdb=" O SERA8 22 " (cutoff:3.500A) Processing helix chain 'A8' and resid 29 through 43 removed outlier: 3.769A pdb=" N PHEA8 36 " --> pdb=" O GLUA8 32 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUA8 37 " --> pdb=" O ASNA8 33 " (cutoff:3.500A) Processing helix chain 'A8' and resid 50 through 71 removed outlier: 3.596A pdb=" N GLNA8 69 " --> pdb=" O LYSA8 65 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYSA8 70 " --> pdb=" O ASPA8 66 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYSA8 71 " --> pdb=" O LEUA8 67 " (cutoff:3.500A) Processing helix chain 'A8' and resid 71 through 81 Processing helix chain 'A8' and resid 92 through 99 removed outlier: 4.038A pdb=" N GLNA8 96 " --> pdb=" O CYSA8 92 " (cutoff:3.500A) Processing helix chain 'AM' and resid 3 through 9 Processing helix chain 'AM' and resid 46 through 112 Proline residue: AM 87 - end of helix Processing helix chain 'B' and resid 23 through 28 removed outlier: 3.952A pdb=" N UNK B 27 " --> pdb=" O UNK B 23 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N UNK B 28 " --> pdb=" O UNK B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 28' Processing helix chain 'C' and resid 5 through 18 removed outlier: 3.668A pdb=" N UNK C 9 " --> pdb=" O UNK C 5 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNK C 10 " --> pdb=" O UNK C 6 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N UNK C 11 " --> pdb=" O UNK C 7 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK C 16 " --> pdb=" O UNK C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 20 No H-bonds generated for 'chain 'C' and resid 20 through 20' Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.583A pdb=" N UNK C 39 " --> pdb=" O UNK C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.814A pdb=" N UNK C 44 " --> pdb=" O UNK C 40 " (cutoff:3.500A) Processing helix chain 'C2' and resid 5 through 24 removed outlier: 4.308A pdb=" N ARGC2 24 " --> pdb=" O SERC2 20 " (cutoff:3.500A) Processing helix chain 'C2' and resid 34 through 73 removed outlier: 3.665A pdb=" N ALAC2 69 " --> pdb=" O GLUC2 65 " (cutoff:3.500A) Processing helix chain 'P2' and resid 82 through 105 Processing helix chain 'S5' and resid 15 through 28 removed outlier: 3.505A pdb=" N CYSS5 28 " --> pdb=" O CYSS5 24 " (cutoff:3.500A) Processing helix chain 'S5' and resid 35 through 47 removed outlier: 3.965A pdb=" N GLUS5 39 " --> pdb=" O GLYS5 35 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASPS5 40 " --> pdb=" O LEUS5 36 " (cutoff:3.500A) Processing helix chain 'S5' and resid 47 through 64 Processing helix chain 'X1' and resid 21 through 28 Processing helix chain 'X1' and resid 30 through 54 Processing helix chain 'X1' and resid 57 through 87 Processing helix chain 'X1' and resid 92 through 99 Processing helix chain 'G1' and resid 4 through 31 Processing helix chain 'G1' and resid 193 through 219 Processing helix chain 'G1' and resid 223 through 233 removed outlier: 3.789A pdb=" N PHEG1 227 " --> pdb=" O GLUG1 223 " (cutoff:3.500A) Processing helix chain 'G2' and resid 3 through 30 Processing helix chain 'G2' and resid 193 through 219 Processing helix chain 'G2' and resid 221 through 237 Processing helix chain 'L2' and resid 210 through 236 Proline residue: L2 218 - end of helix removed outlier: 4.286A pdb=" N LEUL2 236 " --> pdb=" O TYRL2 232 " (cutoff:3.500A) Processing helix chain 'L2' and resid 241 through 253 Processing sheet with id=AA1, first strand: chain 'A2' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A7' and resid 82 through 84 removed outlier: 6.211A pdb=" N ASNS3 29 " --> pdb=" O ARGS3 87 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLNS3 89 " --> pdb=" O ASNS3 29 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHES3 31 " --> pdb=" O GLNS3 89 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N SERS3 91 " --> pdb=" O PHES3 31 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THRS3 33 " --> pdb=" O SERS3 91 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALAS3 92 " --> pdb=" O PHES3 71 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEUS3 78 " --> pdb=" O LEUS3 56 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEUS3 56 " --> pdb=" O LEUS3 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A9' and resid 112 through 114 removed outlier: 6.515A pdb=" N ALAA9 65 " --> pdb=" O LEUA9 90 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VALA9 135 " --> pdb=" O ILEA9 175 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VALA9 177 " --> pdb=" O VALA9 135 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASNA9 137 " --> pdb=" O VALA9 177 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHEA9 174 " --> pdb=" O THRA9 209 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEUA9 211 " --> pdb=" O PHEA9 174 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLNA9 176 " --> pdb=" O LEUA9 211 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILEA9 210 " --> pdb=" O TYRA9 274 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEUA9 276 " --> pdb=" O ILEA9 210 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYSA9 212 " --> pdb=" O LEUA9 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A9' and resid 216 through 217 Processing sheet with id=AA5, first strand: chain 'A9' and resid 246 through 247 Processing sheet with id=AA6, first strand: chain 'AL' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'S1' and resid 83 through 86 removed outlier: 8.984A pdb=" N ILES1 145 " --> pdb=" O GLUS1 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHES1 78 " --> pdb=" O ILES1 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S1' and resid 206 through 208 removed outlier: 3.699A pdb=" N LEUS1 208 " --> pdb=" O VALS1 212 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VALS1 212 " --> pdb=" O LEUS1 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S1' and resid 240 through 243 Processing sheet with id=AB1, first strand: chain 'S1' and resid 289 through 294 removed outlier: 8.227A pdb=" N ASNS1 303 " --> pdb=" O PROS1 318 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARGS1 305 " --> pdb=" O ILES1 316 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILES1 316 " --> pdb=" O ARGS1 305 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASPS1 307 " --> pdb=" O METS1 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S1' and resid 356 through 359 removed outlier: 6.724A pdb=" N VALS1 582 " --> pdb=" O VALS1 602 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLNS1 604 " --> pdb=" O VALS1 582 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEUS1 584 " --> pdb=" O GLNS1 604 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VALS1 382 " --> pdb=" O TYRS1 583 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILES1 381 " --> pdb=" O ASPS1 408 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TRPS1 410 " --> pdb=" O ILES1 381 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLYS1 383 " --> pdb=" O TRPS1 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S1' and resid 484 through 487 removed outlier: 6.171A pdb=" N PHES1 441 " --> pdb=" O GLYS1 471 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILES1 473 " --> pdb=" O PHES1 441 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEUS1 443 " --> pdb=" O ILES1 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S1' and resid 630 through 633 Processing sheet with id=AB5, first strand: chain 'S2' and resid 11 through 15 removed outlier: 6.808A pdb=" N ASNS2 33 " --> pdb=" O VALS2 37 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VALS2 37 " --> pdb=" O ASNS2 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S2' and resid 327 through 332 Processing sheet with id=AB7, first strand: chain 'S3' and resid 155 through 158 Processing sheet with id=AB8, first strand: chain 'S4' and resid 66 through 69 removed outlier: 6.837A pdb=" N VALS4 45 " --> pdb=" O SERS4 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S4' and resid 75 through 76 removed outlier: 3.568A pdb=" N TRPS4 75 " --> pdb=" O SERS4 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S6' and resid 62 through 63 removed outlier: 3.819A pdb=" N VALS6 63 " --> pdb=" O ILES6 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILES6 80 " --> pdb=" O VALS6 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'S7' and resid 83 through 85 removed outlier: 5.818A pdb=" N PHES7 84 " --> pdb=" O ALAS7 123 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N METS7 120 " --> pdb=" O ILES7 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'S8' and resid 111 through 113 Processing sheet with id=AC4, first strand: chain 'S8' and resid 138 through 144 removed outlier: 6.535A pdb=" N GLUS8 143 " --> pdb=" O THRS8 152 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THRS8 152 " --> pdb=" O GLUS8 143 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILES8 157 " --> pdb=" O TYRS8 195 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYRS8 195 " --> pdb=" O ILES8 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V1' and resid 222 through 226 removed outlier: 6.737A pdb=" N LEUV1 141 " --> pdb=" O TYRV1 183 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYRV1 185 " --> pdb=" O LEUV1 141 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VALV1 143 " --> pdb=" O TYRV1 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V1' and resid 314 through 319 removed outlier: 7.965A pdb=" N VALV1 384 " --> pdb=" O CYSV1 305 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SERV1 307 " --> pdb=" O VALV1 384 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASPV1 386 " --> pdb=" O SERV1 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V2' and resid 153 through 155 removed outlier: 6.060A pdb=" N TYRV2 121 " --> pdb=" O SERV2 161 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLYV2 163 " --> pdb=" O TYRV2 121 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEUV2 123 " --> pdb=" O GLYV2 163 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N METV2 165 " --> pdb=" O LEUV2 123 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VALV2 125 " --> pdb=" O METV2 165 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G1' and resid 45 through 46 removed outlier: 7.191A pdb=" N VALG1 89 " --> pdb=" O ASPG1 70 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N HISG1 72 " --> pdb=" O VALG1 89 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLYG1 91 " --> pdb=" O HISG1 72 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEUG1 105 " --> pdb=" O LEUG1 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G1' and resid 54 through 55 removed outlier: 6.371A pdb=" N SERG1 54 " --> pdb=" O VALG1 73 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VALG1 89 " --> pdb=" O ASPG1 70 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N HISG1 72 " --> pdb=" O VALG1 89 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLYG1 91 " --> pdb=" O HISG1 72 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILEG1 121 " --> pdb=" O VALG1 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G1' and resid 60 through 61 removed outlier: 7.074A pdb=" N PHEG1 60 " --> pdb=" O ILEG1 79 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SERG1 78 " --> pdb=" O ILEG1 100 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N METG1 162 " --> pdb=" O TRPG1 181 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VALG1 180 " --> pdb=" O LEUG1 189 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G2' and resid 45 through 46 removed outlier: 3.585A pdb=" N GLYG2 69 " --> pdb=" O METG2 46 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SERG2 66 " --> pdb=" O LEUG2 85 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLYG2 87 " --> pdb=" O SERG2 66 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILEG2 68 " --> pdb=" O GLYG2 87 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VALG2 89 " --> pdb=" O ILEG2 68 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASPG2 70 " --> pdb=" O VALG2 89 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SERG2 91 " --> pdb=" O ASPG2 70 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLNG2 72 " --> pdb=" O SERG2 91 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGG2 93 " --> pdb=" O GLNG2 72 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N THRG2 120 " --> pdb=" O VALG2 89 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SERG2 91 " --> pdb=" O THRG2 120 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILEG2 122 " --> pdb=" O SERG2 91 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARGG2 93 " --> pdb=" O ILEG2 122 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VALG2 121 " --> pdb=" O VALG2 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G2' and resid 54 through 55 removed outlier: 6.512A pdb=" N SERG2 66 " --> pdb=" O LEUG2 85 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLYG2 87 " --> pdb=" O SERG2 66 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILEG2 68 " --> pdb=" O GLYG2 87 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VALG2 89 " --> pdb=" O ILEG2 68 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASPG2 70 " --> pdb=" O VALG2 89 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SERG2 91 " --> pdb=" O ASPG2 70 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLNG2 72 " --> pdb=" O SERG2 91 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGG2 93 " --> pdb=" O GLNG2 72 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VALG2 84 " --> pdb=" O VALG2 106 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VALG2 133 " --> pdb=" O LEUG2 151 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VALG2 150 " --> pdb=" O VALG2 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G2' and resid 60 through 61 removed outlier: 6.778A pdb=" N PHEG2 60 " --> pdb=" O ILEG2 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G2' and resid 99 through 100 removed outlier: 5.912A pdb=" N ASNG2 99 " --> pdb=" O VALG2 128 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THRG2 127 " --> pdb=" O VALG2 145 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHEG2 144 " --> pdb=" O VALG2 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G2' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'L2' and resid 62 through 63 removed outlier: 7.678A pdb=" N LEUL2 106 " --> pdb=" O GLNL2 87 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N THRL2 89 " --> pdb=" O LEUL2 106 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N LYSL2 108 " --> pdb=" O THRL2 89 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VALL2 101 " --> pdb=" O LEUL2 123 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VALL2 122 " --> pdb=" O LEUL2 151 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEUL2 150 " --> pdb=" O LEUL2 168 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILEL2 167 " --> pdb=" O VALL2 186 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L2' and resid 71 through 72 removed outlier: 6.949A pdb=" N LYSL2 71 " --> pdb=" O VALL2 90 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEUL2 106 " --> pdb=" O GLNL2 87 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N THRL2 89 " --> pdb=" O LEUL2 106 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N LYSL2 108 " --> pdb=" O THRL2 89 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THRL2 137 " --> pdb=" O LEUL2 106 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYSL2 108 " --> pdb=" O THRL2 137 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILEL2 139 " --> pdb=" O LYSL2 108 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SERL2 110 " --> pdb=" O ILEL2 139 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SERL2 138 " --> pdb=" O ILEL2 156 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THRL2 155 " --> pdb=" O VALL2 174 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEUL2 173 " --> pdb=" O ILEL2 192 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L2' and resid 77 through 78 removed outlier: 6.910A pdb=" N TYRL2 77 " --> pdb=" O VALL2 96 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SERL2 95 " --> pdb=" O VALL2 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'L2' and resid 179 through 180 removed outlier: 7.263A pdb=" N LEUL2 197 " --> pdb=" O VALL2 206 " (cutoff:3.500A) 2242 hydrogen bonds defined for protein. 6492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.77 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 19382 1.43 - 1.67: 26176 1.67 - 1.90: 423 1.90 - 2.14: 0 2.14 - 2.37: 80 Bond restraints: 46061 Sorted by residual: bond pdb=" O2B NAPA9 401 " pdb=" P2B NAPA9 401 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C4N NAPA9 401 " pdb=" C5N NAPA9 401 " ideal model delta sigma weight residual 1.384 1.482 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C3N NAPA9 401 " pdb=" C4N NAPA9 401 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O5' FMNV1 501 " pdb=" P FMNV1 501 " ideal model delta sigma weight residual 1.676 1.585 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O13 PC1G1 701 " pdb=" P PC1G1 701 " ideal model delta sigma weight residual 1.652 1.588 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 46056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 61998 3.80 - 7.59: 402 7.59 - 11.39: 43 11.39 - 15.19: 16 15.19 - 18.99: 8 Bond angle restraints: 62467 Sorted by residual: angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 89.63 14.70 1.14e+00 7.69e-01 1.66e+02 angle pdb=" S3 SF4S8 302 " pdb="FE2 SF4S8 302 " pdb=" S4 SF4S8 302 " ideal model delta sigma weight residual 104.10 123.09 -18.99 1.50e+00 4.44e-01 1.60e+02 angle pdb=" S1 SF4S8 301 " pdb="FE4 SF4S8 301 " pdb=" S2 SF4S8 301 " ideal model delta sigma weight residual 104.10 123.04 -18.94 1.50e+00 4.44e-01 1.59e+02 angle pdb=" S3 SF4S8 302 " pdb="FE1 SF4S8 302 " pdb=" S4 SF4S8 302 " ideal model delta sigma weight residual 104.10 122.96 -18.86 1.50e+00 4.44e-01 1.58e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 89.50 14.83 1.20e+00 6.94e-01 1.53e+02 ... (remaining 62462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 24604 17.67 - 35.35: 2443 35.35 - 53.02: 414 53.02 - 70.70: 84 70.70 - 88.37: 40 Dihedral angle restraints: 27585 sinusoidal: 11081 harmonic: 16504 Sorted by residual: dihedral pdb=" CA ASPS1 589 " pdb=" C ASPS1 589 " pdb=" N VALS1 590 " pdb=" CA VALS1 590 " ideal model delta harmonic sigma weight residual -180.00 -128.67 -51.33 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA ASPV2 157 " pdb=" C ASPV2 157 " pdb=" N GLYV2 158 " pdb=" CA GLYV2 158 " ideal model delta harmonic sigma weight residual -180.00 -131.56 -48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PHEA7 105 " pdb=" C PHEA7 105 " pdb=" N PROA7 106 " pdb=" CA PROA7 106 " ideal model delta harmonic sigma weight residual 180.00 133.48 46.52 0 5.00e+00 4.00e-02 8.66e+01 ... (remaining 27582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 6922 4.237 - 8.473: 0 8.473 - 12.710: 0 12.710 - 16.946: 0 16.946 - 21.183: 24 Chirality restraints: 6946 Sorted by residual: chirality pdb="FE2 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S3 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S3 SF4S1 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4S8 302 " pdb=" S1 SF4S8 302 " pdb=" S2 SF4S8 302 " pdb=" S4 SF4S8 302 " both_signs ideal model delta sigma weight residual False -10.55 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 6943 not shown) Planarity restraints: 7932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHEA7 105 " -0.066 5.00e-02 4.00e+02 9.89e-02 1.57e+01 pdb=" N PROA7 106 " 0.171 5.00e-02 4.00e+02 pdb=" CA PROA7 106 " -0.052 5.00e-02 4.00e+02 pdb=" CD PROA7 106 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRPG1 80 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C TRPG1 80 " 0.064 2.00e-02 2.50e+03 pdb=" O TRPG1 80 " -0.024 2.00e-02 2.50e+03 pdb=" N TYRG1 81 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGS2 356 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ARGS2 356 " -0.060 2.00e-02 2.50e+03 pdb=" O ARGS2 356 " 0.023 2.00e-02 2.50e+03 pdb=" N ALAS2 357 " 0.020 2.00e-02 2.50e+03 ... (remaining 7929 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 396 2.50 - 3.10: 36172 3.10 - 3.70: 68654 3.70 - 4.30: 95385 4.30 - 4.90: 158977 Nonbonded interactions: 359584 Sorted by model distance: nonbonded pdb=" O TYRS6 92 " pdb="ZN ZNS6 300 " model vdw 1.899 2.230 nonbonded pdb=" O GLNS3 173 " pdb=" OH TYRS7 162 " model vdw 2.016 3.040 nonbonded pdb=" OE1 GLUA5 92 " pdb=" OG1 THRS3 49 " model vdw 2.077 3.040 nonbonded pdb=" OG1 THRS2 109 " pdb=" OH TYRS2 145 " model vdw 2.081 3.040 nonbonded pdb=" OG1 THRA9 219 " pdb=" OE1 GLUA9 220 " model vdw 2.107 3.040 ... (remaining 359579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 53.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.926 46100 Z= 0.391 Angle : 1.017 58.420 62544 Z= 0.520 Chirality : 1.219 21.183 6946 Planarity : 0.005 0.099 7932 Dihedral : 14.468 88.373 16960 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.97 % Favored : 84.80 % Rotamer: Outliers : 0.23 % Allowed : 9.79 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.10), residues: 5572 helix: -1.10 (0.09), residues: 2675 sheet: -2.74 (0.22), residues: 428 loop : -4.24 (0.10), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGS1 119 TYR 0.035 0.002 TYRS7 159 PHE 0.031 0.002 PHEA9 73 TRP 0.039 0.002 TRPS3 18 HIS 0.023 0.001 HISS6 75 Details of bonding type rmsd covalent geometry : bond 0.00709 (46061) covalent geometry : angle 0.89991 (62467) SS BOND : bond 0.00299 ( 7) SS BOND : angle 1.52433 ( 14) hydrogen bonds : bond 0.12567 ( 2233) hydrogen bonds : angle 6.62522 ( 6492) metal coordination : bond 0.32431 ( 32) metal coordination : angle 14.97067 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1470 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A5 88 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A5 106 TRP cc_start: 0.8187 (p90) cc_final: 0.7747 (p90) REVERT: A5 115 TYR cc_start: 0.8105 (t80) cc_final: 0.7392 (t80) REVERT: A6 124 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8513 (tmtp) REVERT: A7 52 GLU cc_start: 0.7348 (mp0) cc_final: 0.7108 (mp0) REVERT: A7 57 PRO cc_start: 0.9135 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7883 (tm-30) REVERT: A7 109 TYR cc_start: 0.9034 (t80) cc_final: 0.8343 (t80) REVERT: A7 115 GLU cc_start: 0.7990 (tt0) cc_final: 0.7737 (tm-30) REVERT: A9 199 GLU cc_start: 0.8895 (tp30) cc_final: 0.7835 (tt0) REVERT: A9 222 ARG cc_start: 0.8486 (mpp80) cc_final: 0.8118 (mtt180) REVERT: A9 291 MET cc_start: 0.9207 (tmm) cc_final: 0.8687 (tmm) REVERT: A9 301 TYR cc_start: 0.7518 (m-80) cc_final: 0.7161 (m-80) REVERT: A9 306 PHE cc_start: 0.7650 (p90) cc_final: 0.7186 (m-80) REVERT: AL 22 ARG cc_start: 0.6809 (mtm180) cc_final: 0.6552 (mpp-170) REVERT: AL 45 ASN cc_start: 0.8477 (m-40) cc_final: 0.8141 (m-40) REVERT: S1 79 VAL cc_start: 0.9433 (t) cc_final: 0.9212 (p) REVERT: S1 80 ASP cc_start: 0.8008 (t70) cc_final: 0.7567 (t70) REVERT: S1 124 GLU cc_start: 0.7969 (pt0) cc_final: 0.7551 (pt0) REVERT: S1 144 LYS cc_start: 0.7712 (mttp) cc_final: 0.7451 (mtpt) REVERT: S1 213 LYS cc_start: 0.8719 (pttp) cc_final: 0.8443 (ptmt) REVERT: S1 285 ASN cc_start: 0.9354 (p0) cc_final: 0.9141 (p0) REVERT: S1 461 LYS cc_start: 0.8871 (tptm) cc_final: 0.8607 (tttm) REVERT: S1 505 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7414 (mttm) REVERT: S1 594 LYS cc_start: 0.8756 (tppt) cc_final: 0.8471 (mttp) REVERT: S1 604 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8442 (tm-30) REVERT: S1 656 LYS cc_start: 0.9105 (mttt) cc_final: 0.8716 (mttm) REVERT: S1 690 ASN cc_start: 0.8641 (t0) cc_final: 0.7964 (t0) REVERT: S1 707 PHE cc_start: 0.7953 (m-80) cc_final: 0.7600 (m-80) REVERT: S2 212 GLN cc_start: 0.8807 (tp40) cc_final: 0.8267 (tp40) REVERT: S2 315 LEU cc_start: 0.9382 (tp) cc_final: 0.9145 (tt) REVERT: S3 1 MET cc_start: 0.7622 (tmm) cc_final: 0.6778 (tmm) REVERT: S3 94 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6918 (mt-10) REVERT: S3 118 MET cc_start: 0.8958 (mmp) cc_final: 0.8652 (mmp) REVERT: S3 167 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7131 (mt-10) REVERT: S4 55 SER cc_start: 0.9012 (m) cc_final: 0.8799 (m) REVERT: S4 94 ASP cc_start: 0.9256 (p0) cc_final: 0.8985 (p0) REVERT: S4 111 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8615 (tttt) REVERT: S4 129 LYS cc_start: 0.8867 (mttt) cc_final: 0.8482 (mttm) REVERT: S7 203 ARG cc_start: 0.8503 (ptt-90) cc_final: 0.8248 (ptt-90) REVERT: S8 49 ARG cc_start: 0.8634 (ttm170) cc_final: 0.7108 (tpt170) REVERT: S8 85 LYS cc_start: 0.9202 (tmmt) cc_final: 0.8901 (tttt) REVERT: S8 189 THR cc_start: 0.8831 (p) cc_final: 0.8581 (p) REVERT: S8 210 GLU cc_start: 0.9104 (tp30) cc_final: 0.8527 (tp30) REVERT: V1 144 ASN cc_start: 0.9369 (t0) cc_final: 0.9080 (t0) REVERT: V1 165 LYS cc_start: 0.9023 (tppt) cc_final: 0.8542 (mmtm) REVERT: V1 198 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7494 (tm-30) REVERT: V1 268 THR cc_start: 0.8571 (p) cc_final: 0.8371 (p) REVERT: V1 297 ASN cc_start: 0.8730 (m110) cc_final: 0.8140 (t0) REVERT: V1 367 TYR cc_start: 0.8244 (m-80) cc_final: 0.7859 (m-80) REVERT: V2 95 ILE cc_start: 0.9093 (tp) cc_final: 0.8853 (tt) REVERT: V2 137 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8137 (mtt180) REVERT: V2 165 MET cc_start: 0.8533 (ttt) cc_final: 0.8309 (ttp) REVERT: V2 168 MET cc_start: 0.7836 (mtp) cc_final: 0.7593 (mtm) REVERT: V2 176 MET cc_start: 0.8558 (ppp) cc_final: 0.8342 (ppp) REVERT: V2 195 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7200 (mt-10) REVERT: 1M 82 PHE cc_start: 0.9200 (t80) cc_final: 0.8979 (t80) REVERT: 1M 262 ARG cc_start: 0.8399 (tpt170) cc_final: 0.8078 (mtt180) REVERT: 2M 207 ILE cc_start: 0.6890 (mm) cc_final: 0.6273 (mm) REVERT: 2M 244 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8571 (tm-30) REVERT: 2M 301 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8620 (mm-40) REVERT: 2M 303 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8165 (mmtt) REVERT: 2M 344 MET cc_start: 0.8952 (mtm) cc_final: 0.8695 (mtt) REVERT: 2M 347 ASP cc_start: 0.8716 (t70) cc_final: 0.8507 (t0) REVERT: 2M 436 MET cc_start: 0.8093 (mmm) cc_final: 0.6745 (tmm) REVERT: 2M 439 ASP cc_start: 0.8265 (t70) cc_final: 0.8047 (t0) REVERT: 2M 444 TRP cc_start: 0.7773 (p-90) cc_final: 0.7543 (p-90) REVERT: 3M 96 MET cc_start: 0.8909 (mmp) cc_final: 0.8584 (mmt) REVERT: 4L 6 TYR cc_start: 0.8882 (m-80) cc_final: 0.8576 (m-80) REVERT: 4L 26 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7311 (mmm160) REVERT: 4L 82 ILE cc_start: 0.8986 (tp) cc_final: 0.8747 (tp) REVERT: 6M 70 MET cc_start: 0.9163 (mmp) cc_final: 0.8726 (mmt) REVERT: 6M 167 ILE cc_start: 0.9326 (mm) cc_final: 0.9086 (mm) REVERT: A1 4 ARG cc_start: 0.8658 (tpp-160) cc_final: 0.8416 (tpp-160) REVERT: A1 54 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9129 (tttp) REVERT: A1 58 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8417 (mt-10) REVERT: A8 45 ASN cc_start: 0.8951 (t0) cc_final: 0.8469 (t0) REVERT: A8 55 ASP cc_start: 0.7819 (t0) cc_final: 0.7556 (t0) REVERT: A8 75 MET cc_start: 0.9146 (ttt) cc_final: 0.8917 (tpp) REVERT: A8 87 ASN cc_start: 0.9442 (m-40) cc_final: 0.9228 (m-40) REVERT: C2 34 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C2 62 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8835 (ttmm) REVERT: C2 63 MET cc_start: 0.8854 (tpp) cc_final: 0.8541 (tpp) REVERT: S5 49 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8385 (ttpt) REVERT: X1 10 LYS cc_start: 0.8918 (mttt) cc_final: 0.8675 (mttp) REVERT: G1 16 ARG cc_start: 0.9126 (mtp-110) cc_final: 0.8724 (ttp-170) REVERT: G1 23 ASP cc_start: 0.8504 (t0) cc_final: 0.8024 (t0) REVERT: G1 38 GLN cc_start: 0.9186 (mp10) cc_final: 0.8966 (mp10) REVERT: G1 80 TRP cc_start: 0.8892 (m100) cc_final: 0.8595 (m100) REVERT: G1 181 TRP cc_start: 0.8205 (m100) cc_final: 0.7761 (m100) REVERT: G1 209 ASN cc_start: 0.8393 (m-40) cc_final: 0.7995 (m-40) REVERT: G2 4 LEU cc_start: 0.8780 (tp) cc_final: 0.8555 (pp) REVERT: G2 212 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8652 (tm-30) REVERT: G2 229 LYS cc_start: 0.9497 (ttpt) cc_final: 0.9282 (ttpp) REVERT: L2 165 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.8214 (m170) outliers start: 11 outliers final: 4 residues processed: 1480 average time/residue: 0.2593 time to fit residues: 624.6936 Evaluate side-chains 1245 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1240 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S8 residue 126 CYS Chi-restraints excluded: chain V1 residue 155 ASP Chi-restraints excluded: chain G2 residue 141 ASP Chi-restraints excluded: chain L2 residue 165 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 394 optimal weight: 0.0010 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.6980 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2 20 GLN A2 43 ASN A7 45 GLN A7 58 ASN A9 48 HIS A9 80 GLN A9 88 GLN A9 133 ASN ** A9 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 137 HIS S1 109 HIS S1 117 ASN S1 485 HIS ** S1 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 527 GLN S1 571 GLN ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 683 ASN S2 78 GLN S2 113 ASN S2 121 HIS S2 213 GLN S2 280 ASN ** S2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 4 GLN S3 27 HIS S3 29 ASN S4 57 GLN S4 73 GLN S6 99 GLN S6 102 HIS S7 72 ASN S8 111 HIS V1 226 HIS V1 298 ASN V1 450 HIS V1 464 GLN V2 37 ASN ** V2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 122 HIS V2 221 ASN ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 197 GLN 2M 236 HIS 2M 265 ASN 2M 332 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6M 22 ASN A1 2 ASN A1 39 HIS A8 10 ASN A8 24 HIS ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 102 HIS C2 35 HIS C2 71 ASN P2 86 ASN ** X1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 99 ASN G1 212 GLN G2 218 ASN L2 107 ASN ** L2 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.126213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.103738 restraints weight = 67625.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.106492 restraints weight = 39871.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.108352 restraints weight = 28236.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109503 restraints weight = 22421.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110388 restraints weight = 19297.115| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.253 46100 Z= 0.337 Angle : 2.123 58.678 62544 Z= 1.248 Chirality : 0.377 6.684 6946 Planarity : 0.006 0.093 7932 Dihedral : 8.150 85.773 6488 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.95 % Favored : 88.94 % Rotamer: Outliers : 2.72 % Allowed : 17.56 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.11), residues: 5572 helix: 0.39 (0.10), residues: 2688 sheet: -2.03 (0.25), residues: 410 loop : -3.69 (0.10), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGS5 27 TYR 0.033 0.002 TYRS7 159 PHE 0.037 0.002 PHEAM 30 TRP 0.026 0.001 TRPAM 130 HIS 0.015 0.001 HISA8 24 Details of bonding type rmsd covalent geometry : bond 0.00951 (46061) covalent geometry : angle 1.92530 (62467) SS BOND : bond 0.00510 ( 7) SS BOND : angle 3.74237 ( 14) hydrogen bonds : bond 0.05516 ( 2233) hydrogen bonds : angle 5.38490 ( 6492) metal coordination : bond 0.04390 ( 32) metal coordination : angle 28.23717 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1433 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A5 88 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A5 115 TYR cc_start: 0.7979 (t80) cc_final: 0.7443 (t80) REVERT: A6 124 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8481 (tmtp) REVERT: A7 52 GLU cc_start: 0.7408 (mp0) cc_final: 0.7061 (mp0) REVERT: A7 57 PRO cc_start: 0.8966 (Cg_exo) cc_final: 0.8701 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7929 (tm-30) REVERT: A7 109 TYR cc_start: 0.8996 (t80) cc_final: 0.8252 (t80) REVERT: A7 115 GLU cc_start: 0.7875 (tt0) cc_final: 0.7644 (tm-30) REVERT: A9 222 ARG cc_start: 0.8435 (mpp80) cc_final: 0.7947 (mtt180) REVERT: A9 265 ASP cc_start: 0.6632 (m-30) cc_final: 0.6405 (m-30) REVERT: A9 306 PHE cc_start: 0.7590 (p90) cc_final: 0.7111 (m-10) REVERT: AL 45 ASN cc_start: 0.8284 (m-40) cc_final: 0.7655 (t0) REVERT: AL 71 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7833 (ptm160) REVERT: AL 77 TYR cc_start: 0.8811 (m-80) cc_final: 0.8500 (m-80) REVERT: S1 117 ASN cc_start: 0.8558 (t0) cc_final: 0.8075 (t0) REVERT: S1 124 GLU cc_start: 0.7927 (pt0) cc_final: 0.7577 (pt0) REVERT: S1 144 LYS cc_start: 0.7367 (mttp) cc_final: 0.6933 (mtpt) REVERT: S1 165 MET cc_start: 0.8780 (tmm) cc_final: 0.8437 (ttp) REVERT: S1 231 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7993 (mt-10) REVERT: S1 300 VAL cc_start: 0.9133 (m) cc_final: 0.8911 (p) REVERT: S1 461 LYS cc_start: 0.9034 (tptm) cc_final: 0.8601 (tttm) REVERT: S1 505 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7698 (mtpp) REVERT: S1 594 LYS cc_start: 0.8569 (tppt) cc_final: 0.8171 (mmtp) REVERT: S1 604 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8494 (tm-30) REVERT: S1 690 ASN cc_start: 0.8762 (t0) cc_final: 0.7991 (t0) REVERT: S1 707 PHE cc_start: 0.7867 (m-80) cc_final: 0.7604 (m-80) REVERT: S2 212 GLN cc_start: 0.8637 (tp40) cc_final: 0.7942 (tp40) REVERT: S2 301 ARG cc_start: 0.8168 (mpp-170) cc_final: 0.7543 (mtm-85) REVERT: S3 1 MET cc_start: 0.7659 (tmm) cc_final: 0.6972 (tmm) REVERT: S3 63 ASP cc_start: 0.9340 (t70) cc_final: 0.9106 (t0) REVERT: S3 91 SER cc_start: 0.9315 (t) cc_final: 0.8996 (p) REVERT: S3 94 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7151 (mt-10) REVERT: S3 167 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6954 (mt-10) REVERT: S7 61 GLU cc_start: 0.7814 (tt0) cc_final: 0.7599 (tt0) REVERT: S8 46 ASP cc_start: 0.9070 (m-30) cc_final: 0.8754 (m-30) REVERT: S8 49 ARG cc_start: 0.8584 (ttm170) cc_final: 0.7120 (tpt170) REVERT: S8 51 GLN cc_start: 0.9232 (tt0) cc_final: 0.8964 (tp40) REVERT: S8 59 ASP cc_start: 0.8546 (p0) cc_final: 0.8223 (p0) REVERT: S8 85 LYS cc_start: 0.8930 (tmmt) cc_final: 0.8554 (tttt) REVERT: S8 189 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8826 (p) REVERT: S8 208 GLU cc_start: 0.8936 (tp30) cc_final: 0.8678 (tp30) REVERT: V1 219 TYR cc_start: 0.7802 (t80) cc_final: 0.7104 (t80) REVERT: V1 297 ASN cc_start: 0.8605 (m110) cc_final: 0.8010 (t0) REVERT: V1 367 TYR cc_start: 0.8024 (m-80) cc_final: 0.7560 (m-80) REVERT: V1 435 GLU cc_start: 0.8794 (mp0) cc_final: 0.8231 (mp0) REVERT: V2 53 VAL cc_start: 0.9548 (t) cc_final: 0.9307 (p) REVERT: V2 78 GLN cc_start: 0.8849 (mt0) cc_final: 0.8549 (mt0) REVERT: V2 95 ILE cc_start: 0.8912 (tp) cc_final: 0.8702 (tt) REVERT: V2 168 MET cc_start: 0.8067 (mtp) cc_final: 0.7807 (mtm) REVERT: V2 176 MET cc_start: 0.8766 (ppp) cc_final: 0.8357 (ppp) REVERT: V2 195 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7092 (mt-10) REVERT: 1M 98 MET cc_start: 0.8839 (ttm) cc_final: 0.8584 (ttm) REVERT: 1M 102 ASP cc_start: 0.8424 (t0) cc_final: 0.8060 (t0) REVERT: 1M 262 ARG cc_start: 0.8333 (tpt170) cc_final: 0.7999 (mtt90) REVERT: 2M 179 LEU cc_start: 0.9543 (tp) cc_final: 0.9304 (tt) REVERT: 2M 201 ILE cc_start: 0.9566 (tt) cc_final: 0.9311 (tt) REVERT: 2M 243 TYR cc_start: 0.7929 (m-10) cc_final: 0.7629 (m-10) REVERT: 2M 244 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8415 (tm-30) REVERT: 2M 299 MET cc_start: 0.8265 (tmm) cc_final: 0.7907 (tmm) REVERT: 2M 347 ASP cc_start: 0.8591 (t70) cc_final: 0.8330 (t0) REVERT: 2M 436 MET cc_start: 0.7992 (mmm) cc_final: 0.6499 (ppp) REVERT: 2M 439 ASP cc_start: 0.8225 (t70) cc_final: 0.8020 (t0) REVERT: 3M 96 MET cc_start: 0.8844 (mmp) cc_final: 0.8395 (mmt) REVERT: 4L 6 TYR cc_start: 0.8910 (m-80) cc_final: 0.8624 (m-80) REVERT: 4L 77 LEU cc_start: 0.9069 (tp) cc_final: 0.8776 (tp) REVERT: 4L 82 ILE cc_start: 0.8917 (tp) cc_final: 0.8705 (tp) REVERT: A1 4 ARG cc_start: 0.8815 (tpp-160) cc_final: 0.8538 (tpp-160) REVERT: A1 49 MET cc_start: 0.8591 (mmp) cc_final: 0.8045 (mmm) REVERT: A8 45 ASN cc_start: 0.8961 (t0) cc_final: 0.8207 (t0) REVERT: A8 74 GLU cc_start: 0.8858 (mp0) cc_final: 0.8412 (mt-10) REVERT: A8 75 MET cc_start: 0.9224 (ttt) cc_final: 0.8884 (tpp) REVERT: C2 62 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8846 (ttmm) REVERT: C2 63 MET cc_start: 0.8921 (tpp) cc_final: 0.8659 (mtm) REVERT: P2 105 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8217 (mmmm) REVERT: X1 10 LYS cc_start: 0.8899 (mttt) cc_final: 0.8544 (mttp) REVERT: G1 16 ARG cc_start: 0.9012 (mtp-110) cc_final: 0.8715 (ttp-170) REVERT: G1 80 TRP cc_start: 0.9281 (m100) cc_final: 0.8777 (m100) REVERT: G1 181 TRP cc_start: 0.8119 (m100) cc_final: 0.7633 (m100) REVERT: G1 206 ASN cc_start: 0.8514 (m-40) cc_final: 0.8209 (m110) REVERT: G1 209 ASN cc_start: 0.8302 (m-40) cc_final: 0.7981 (m-40) REVERT: G2 56 ASP cc_start: 0.8927 (t0) cc_final: 0.8691 (t0) REVERT: G2 70 ASP cc_start: 0.8421 (p0) cc_final: 0.8205 (p0) REVERT: G2 86 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8515 (ttp80) REVERT: G2 155 VAL cc_start: 0.8569 (p) cc_final: 0.8352 (p) REVERT: G2 228 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7327 (mt-10) REVERT: L2 83 VAL cc_start: 0.9333 (t) cc_final: 0.9015 (p) REVERT: L2 181 GLU cc_start: 0.8294 (tt0) cc_final: 0.8044 (tt0) REVERT: L2 196 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8091 (mm-30) REVERT: L2 235 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8114 (t80) REVERT: L2 246 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7714 (tm-30) outliers start: 129 outliers final: 72 residues processed: 1512 average time/residue: 0.2606 time to fit residues: 647.3659 Evaluate side-chains 1335 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1261 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 111 VAL Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 190 MET Chi-restraints excluded: chain A9 residue 202 LEU Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain AL residue 53 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 214 THR Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 523 GLU Chi-restraints excluded: chain S2 residue 209 VAL Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 310 ILE Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 126 LEU Chi-restraints excluded: chain S7 residue 137 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 189 THR Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 142 VAL Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 429 VAL Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 464 GLN Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain 1M residue 240 SER Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 3M residue 21 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 82 VAL Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 146 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 49 ILE Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 20 SER Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain X1 residue 53 ILE Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 188 PHE Chi-restraints excluded: chain L2 residue 46 THR Chi-restraints excluded: chain L2 residue 122 VAL Chi-restraints excluded: chain L2 residue 235 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 23 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 495 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 434 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 542 optimal weight: 0.7980 chunk 427 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 119 ASN A9 133 ASN AL 137 HIS ** S1 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 683 ASN S2 48 HIS S2 99 GLN S2 165 GLN S2 213 GLN S2 280 ASN S3 125 ASN S4 73 GLN ** S7 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 464 GLN ** V2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 212 GLN G2 218 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.103501 restraints weight = 67217.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.106210 restraints weight = 39891.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.108008 restraints weight = 28427.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.109223 restraints weight = 22699.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.110010 restraints weight = 19466.737| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.245 46100 Z= 0.348 Angle : 2.123 59.208 62544 Z= 1.245 Chirality : 0.373 6.401 6946 Planarity : 0.005 0.094 7932 Dihedral : 7.826 87.200 6481 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 4.15 % Allowed : 19.65 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.11), residues: 5572 helix: 0.84 (0.10), residues: 2686 sheet: -1.77 (0.26), residues: 405 loop : -3.39 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGS5 27 TYR 0.045 0.002 TYR2M 149 PHE 0.029 0.002 PHEAM 30 TRP 0.025 0.001 TRPC2 33 HIS 0.007 0.001 HIS2M 69 Details of bonding type rmsd covalent geometry : bond 0.00993 (46061) covalent geometry : angle 1.91928 (62467) SS BOND : bond 0.00985 ( 7) SS BOND : angle 4.13744 ( 14) hydrogen bonds : bond 0.05244 ( 2233) hydrogen bonds : angle 5.24454 ( 6492) metal coordination : bond 0.03156 ( 32) metal coordination : angle 28.61130 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1335 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 87 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A5 88 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A6 124 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8535 (tmtp) REVERT: A7 52 GLU cc_start: 0.7404 (mp0) cc_final: 0.6922 (mp0) REVERT: A7 57 PRO cc_start: 0.9005 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7847 (tm-30) REVERT: A7 109 TYR cc_start: 0.8977 (t80) cc_final: 0.8235 (t80) REVERT: A7 115 GLU cc_start: 0.7906 (tt0) cc_final: 0.7662 (tm-30) REVERT: A9 199 GLU cc_start: 0.8835 (tp30) cc_final: 0.7846 (tt0) REVERT: A9 222 ARG cc_start: 0.8385 (mpp80) cc_final: 0.7924 (mtt180) REVERT: A9 265 ASP cc_start: 0.6670 (m-30) cc_final: 0.6457 (m-30) REVERT: A9 306 PHE cc_start: 0.7546 (p90) cc_final: 0.6990 (m-10) REVERT: AL 71 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7796 (ptm160) REVERT: AL 77 TYR cc_start: 0.8823 (m-80) cc_final: 0.8479 (m-80) REVERT: S1 88 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8127 (mmtm) REVERT: S1 117 ASN cc_start: 0.8497 (t0) cc_final: 0.8069 (t0) REVERT: S1 124 GLU cc_start: 0.8031 (pt0) cc_final: 0.7682 (pt0) REVERT: S1 165 MET cc_start: 0.8753 (tmm) cc_final: 0.8456 (ttp) REVERT: S1 231 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8024 (mt-10) REVERT: S1 300 VAL cc_start: 0.9094 (m) cc_final: 0.8886 (p) REVERT: S1 461 LYS cc_start: 0.9039 (tptm) cc_final: 0.8617 (tttm) REVERT: S1 556 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8448 (pp) REVERT: S1 604 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8120 (tm-30) REVERT: S1 690 ASN cc_start: 0.8848 (t0) cc_final: 0.8032 (t0) REVERT: S1 694 ARG cc_start: 0.7924 (ptm-80) cc_final: 0.7691 (ptm-80) REVERT: S1 707 PHE cc_start: 0.7843 (m-80) cc_final: 0.7587 (m-80) REVERT: S2 139 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8023 (mm-30) REVERT: S2 212 GLN cc_start: 0.8666 (tp40) cc_final: 0.8107 (tp40) REVERT: S2 223 MET cc_start: 0.9357 (mmm) cc_final: 0.9097 (mmm) REVERT: S2 247 PHE cc_start: 0.8925 (p90) cc_final: 0.8626 (p90) REVERT: S3 1 MET cc_start: 0.7675 (tmm) cc_final: 0.7249 (tmm) REVERT: S3 17 LYS cc_start: 0.9440 (ttpp) cc_final: 0.9232 (ttpp) REVERT: S3 84 SER cc_start: 0.9066 (m) cc_final: 0.8788 (t) REVERT: S3 91 SER cc_start: 0.9348 (t) cc_final: 0.8946 (p) REVERT: S7 211 TRP cc_start: 0.8924 (t-100) cc_final: 0.8647 (t-100) REVERT: S8 49 ARG cc_start: 0.8640 (ttm170) cc_final: 0.7070 (tpt170) REVERT: S8 51 GLN cc_start: 0.9184 (tt0) cc_final: 0.8946 (tp40) REVERT: S8 59 ASP cc_start: 0.8514 (p0) cc_final: 0.8172 (p0) REVERT: S8 85 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8575 (tttt) REVERT: S8 189 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.7259 (p) REVERT: S8 192 GLU cc_start: 0.8642 (mp0) cc_final: 0.7917 (mp0) REVERT: S8 208 GLU cc_start: 0.8945 (tp30) cc_final: 0.8668 (tp30) REVERT: S8 213 GLU cc_start: 0.8777 (tp30) cc_final: 0.8445 (tp30) REVERT: V1 68 ARG cc_start: 0.8727 (mtt90) cc_final: 0.8524 (mtt90) REVERT: V1 165 LYS cc_start: 0.8989 (tppt) cc_final: 0.8622 (mmtm) REVERT: V1 190 TYR cc_start: 0.8747 (m-80) cc_final: 0.8412 (m-80) REVERT: V1 219 TYR cc_start: 0.7770 (t80) cc_final: 0.7069 (t80) REVERT: V1 268 THR cc_start: 0.8708 (p) cc_final: 0.8410 (p) REVERT: V1 297 ASN cc_start: 0.8650 (m110) cc_final: 0.8090 (t0) REVERT: V1 367 TYR cc_start: 0.8086 (m-80) cc_final: 0.7591 (m-80) REVERT: V1 415 GLU cc_start: 0.8340 (mp0) cc_final: 0.7967 (mp0) REVERT: V1 435 GLU cc_start: 0.8810 (mp0) cc_final: 0.8209 (mp0) REVERT: V1 455 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8850 (tt) REVERT: V2 53 VAL cc_start: 0.9535 (t) cc_final: 0.9306 (p) REVERT: V2 78 GLN cc_start: 0.8993 (mt0) cc_final: 0.8613 (mt0) REVERT: V2 176 MET cc_start: 0.8807 (ppp) cc_final: 0.8518 (ppp) REVERT: V2 195 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7068 (mt-10) REVERT: 1M 102 ASP cc_start: 0.8504 (t0) cc_final: 0.8164 (t0) REVERT: 1M 262 ARG cc_start: 0.8329 (tpt170) cc_final: 0.8017 (mtt180) REVERT: 2M 113 GLU cc_start: 0.8443 (mp0) cc_final: 0.8198 (mp0) REVERT: 2M 179 LEU cc_start: 0.9555 (tp) cc_final: 0.9305 (tt) REVERT: 2M 243 TYR cc_start: 0.7900 (m-10) cc_final: 0.7558 (m-80) REVERT: 2M 244 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8394 (tm-30) REVERT: 2M 265 ASN cc_start: 0.9301 (t160) cc_final: 0.9087 (t0) REVERT: 2M 299 MET cc_start: 0.8287 (tmm) cc_final: 0.7915 (tmm) REVERT: 2M 347 ASP cc_start: 0.8710 (t70) cc_final: 0.8413 (t0) REVERT: 2M 434 LYS cc_start: 0.7270 (mmtm) cc_final: 0.6781 (tmtt) REVERT: 2M 436 MET cc_start: 0.7902 (mmm) cc_final: 0.6448 (ppp) REVERT: 3M 96 MET cc_start: 0.8852 (mmp) cc_final: 0.8366 (mmt) REVERT: 3M 115 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8929 (pp) REVERT: 4L 6 TYR cc_start: 0.8944 (m-80) cc_final: 0.8622 (m-80) REVERT: 4L 77 LEU cc_start: 0.9080 (tp) cc_final: 0.8739 (tp) REVERT: 4L 82 ILE cc_start: 0.8897 (tp) cc_final: 0.8696 (tp) REVERT: A1 4 ARG cc_start: 0.8808 (tpp-160) cc_final: 0.8520 (tpp-160) REVERT: A1 36 ARG cc_start: 0.9159 (ptt90) cc_final: 0.8653 (ptt180) REVERT: A1 49 MET cc_start: 0.8591 (mmp) cc_final: 0.8109 (mmm) REVERT: A8 45 ASN cc_start: 0.8903 (t0) cc_final: 0.8199 (t0) REVERT: A8 74 GLU cc_start: 0.8846 (mp0) cc_final: 0.8418 (mt-10) REVERT: A8 75 MET cc_start: 0.9235 (ttt) cc_final: 0.8900 (tpp) REVERT: C2 26 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9210 (pp) REVERT: P2 105 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8187 (mmmm) REVERT: S5 11 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8517 (ttmm) REVERT: S5 49 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8344 (ttpt) REVERT: X1 10 LYS cc_start: 0.8847 (mttt) cc_final: 0.7952 (mttp) REVERT: G1 16 ARG cc_start: 0.8979 (mtp-110) cc_final: 0.8719 (ttp-170) REVERT: G1 38 GLN cc_start: 0.9141 (mp10) cc_final: 0.8905 (mp10) REVERT: G1 80 TRP cc_start: 0.9262 (m100) cc_final: 0.8781 (m100) REVERT: G1 102 ASP cc_start: 0.8787 (p0) cc_final: 0.8487 (p0) REVERT: G1 128 VAL cc_start: 0.9319 (t) cc_final: 0.8929 (p) REVERT: G1 206 ASN cc_start: 0.8511 (m-40) cc_final: 0.8196 (m-40) REVERT: G1 209 ASN cc_start: 0.8220 (m-40) cc_final: 0.8009 (m-40) REVERT: G2 56 ASP cc_start: 0.9025 (t70) cc_final: 0.8819 (t0) REVERT: G2 86 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8416 (ttp80) REVERT: G2 101 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8260 (mm-40) REVERT: G2 140 GLU cc_start: 0.7020 (mp0) cc_final: 0.6607 (mp0) REVERT: G2 155 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8215 (p) REVERT: L2 83 VAL cc_start: 0.9323 (t) cc_final: 0.9071 (p) REVERT: L2 165 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8285 (m170) REVERT: L2 235 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8190 (t80) outliers start: 197 outliers final: 121 residues processed: 1453 average time/residue: 0.2542 time to fit residues: 611.5596 Evaluate side-chains 1366 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1237 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A2 residue 88 ASP Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 111 VAL Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 153 VAL Chi-restraints excluded: chain A9 residue 190 MET Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 53 VAL Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 169 LEU Chi-restraints excluded: chain S1 residue 214 THR Chi-restraints excluded: chain S1 residue 265 VAL Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 588 ASP Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S2 residue 209 VAL Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 310 ILE Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 121 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 167 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 189 THR Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 142 VAL Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 270 VAL Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 455 LEU Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain 1M residue 64 ILE Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 1M residue 254 ILE Chi-restraints excluded: chain 1M residue 280 TYR Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 465 ILE Chi-restraints excluded: chain 3M residue 21 LEU Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 103 THR Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 143 LEU Chi-restraints excluded: chain 6M residue 146 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A1 residue 40 ILE Chi-restraints excluded: chain A8 residue 32 GLU Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 20 SER Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 14 CYS Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 141 ASP Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 155 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 218 ASN Chi-restraints excluded: chain L2 residue 46 THR Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 122 VAL Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 235 PHE Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 457 optimal weight: 0.1980 chunk 330 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 536 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A7 98 GLN AL 72 HIS AL 137 HIS S1 549 ASN ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 683 ASN S2 113 ASN S2 280 ASN S4 73 GLN ** S7 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 464 GLN ** V2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 42 HIS G1 212 GLN L2 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.129302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.106670 restraints weight = 67254.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109499 restraints weight = 39204.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111398 restraints weight = 27595.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112579 restraints weight = 21839.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113500 restraints weight = 18727.255| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.248 46100 Z= 0.342 Angle : 2.121 58.599 62544 Z= 1.242 Chirality : 0.372 6.348 6946 Planarity : 0.005 0.093 7932 Dihedral : 7.515 89.537 6481 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.50 % Favored : 89.39 % Rotamer: Outliers : 4.44 % Allowed : 21.14 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5572 helix: 1.06 (0.10), residues: 2696 sheet: -1.77 (0.26), residues: 421 loop : -3.18 (0.11), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGV1 330 TYR 0.058 0.001 TYR2M 149 PHE 0.026 0.001 PHEAM 30 TRP 0.018 0.001 TRPAM 130 HIS 0.005 0.001 HIS2M 69 Details of bonding type rmsd covalent geometry : bond 0.00984 (46061) covalent geometry : angle 1.91340 (62467) SS BOND : bond 0.00572 ( 7) SS BOND : angle 3.81057 ( 14) hydrogen bonds : bond 0.04844 ( 2233) hydrogen bonds : angle 5.10147 ( 6492) metal coordination : bond 0.02308 ( 32) metal coordination : angle 28.82991 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1552 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1341 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 87 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A5 88 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A6 124 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8583 (tttp) REVERT: A7 52 GLU cc_start: 0.7383 (mp0) cc_final: 0.6932 (mp0) REVERT: A7 57 PRO cc_start: 0.8994 (Cg_exo) cc_final: 0.8747 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7855 (tm-30) REVERT: A7 109 TYR cc_start: 0.8943 (t80) cc_final: 0.8225 (t80) REVERT: A7 115 GLU cc_start: 0.7877 (tt0) cc_final: 0.7670 (tm-30) REVERT: A9 222 ARG cc_start: 0.8374 (mpp80) cc_final: 0.7911 (mtt180) REVERT: A9 306 PHE cc_start: 0.7586 (p90) cc_final: 0.6933 (m-10) REVERT: AL 45 ASN cc_start: 0.8394 (m-40) cc_final: 0.8122 (m-40) REVERT: AL 71 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7765 (ptm160) REVERT: AL 77 TYR cc_start: 0.8844 (m-80) cc_final: 0.8521 (m-80) REVERT: S1 88 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8187 (mmtm) REVERT: S1 117 ASN cc_start: 0.8339 (t0) cc_final: 0.7915 (t0) REVERT: S1 124 GLU cc_start: 0.8051 (pt0) cc_final: 0.7676 (pt0) REVERT: S1 165 MET cc_start: 0.8663 (tmm) cc_final: 0.8247 (ttt) REVERT: S1 231 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7970 (mt-10) REVERT: S1 371 ASP cc_start: 0.7763 (t0) cc_final: 0.7526 (t70) REVERT: S1 461 LYS cc_start: 0.9021 (tptm) cc_final: 0.8579 (tttm) REVERT: S1 526 ASP cc_start: 0.8556 (p0) cc_final: 0.8334 (p0) REVERT: S1 556 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8442 (pp) REVERT: S1 604 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8681 (tm-30) REVERT: S1 690 ASN cc_start: 0.8866 (t0) cc_final: 0.8100 (t0) REVERT: S1 707 PHE cc_start: 0.7806 (m-80) cc_final: 0.7582 (m-80) REVERT: S1 725 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5721 (mmp) REVERT: S2 87 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8506 (mt-10) REVERT: S2 139 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7953 (mm-30) REVERT: S2 143 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8598 (tm-30) REVERT: S2 166 ASP cc_start: 0.8648 (t70) cc_final: 0.8167 (t0) REVERT: S2 212 GLN cc_start: 0.8645 (tp40) cc_final: 0.8109 (tp40) REVERT: S2 223 MET cc_start: 0.9348 (mmm) cc_final: 0.9056 (mmm) REVERT: S2 301 ARG cc_start: 0.8096 (mpp-170) cc_final: 0.7363 (mtm-85) REVERT: S3 1 MET cc_start: 0.7614 (tmm) cc_final: 0.7199 (tmm) REVERT: S3 23 GLU cc_start: 0.8677 (tt0) cc_final: 0.8076 (tt0) REVERT: S3 30 ARG cc_start: 0.9020 (mtp-110) cc_final: 0.8755 (ttp80) REVERT: S3 84 SER cc_start: 0.9052 (m) cc_final: 0.8753 (t) REVERT: S3 91 SER cc_start: 0.9341 (t) cc_final: 0.8948 (p) REVERT: S3 167 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6953 (mt-10) REVERT: S8 49 ARG cc_start: 0.8651 (ttm170) cc_final: 0.7045 (tpt170) REVERT: S8 50 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8139 (mt-10) REVERT: S8 59 ASP cc_start: 0.8484 (p0) cc_final: 0.8073 (p0) REVERT: S8 85 LYS cc_start: 0.8904 (tmmt) cc_final: 0.8500 (tttt) REVERT: S8 158 ASP cc_start: 0.8690 (p0) cc_final: 0.8444 (p0) REVERT: S8 208 GLU cc_start: 0.8886 (tp30) cc_final: 0.8592 (tp30) REVERT: S8 213 GLU cc_start: 0.8741 (tp30) cc_final: 0.8370 (tp30) REVERT: V1 68 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8313 (mtt90) REVERT: V1 130 MET cc_start: 0.8724 (tpp) cc_final: 0.8501 (mmt) REVERT: V1 162 ASP cc_start: 0.8412 (t0) cc_final: 0.8145 (t70) REVERT: V1 165 LYS cc_start: 0.8773 (tppt) cc_final: 0.8570 (mmtm) REVERT: V1 190 TYR cc_start: 0.8638 (m-80) cc_final: 0.8215 (m-80) REVERT: V1 268 THR cc_start: 0.8746 (p) cc_final: 0.8481 (p) REVERT: V1 297 ASN cc_start: 0.8641 (m110) cc_final: 0.8110 (t0) REVERT: V1 367 TYR cc_start: 0.8053 (m-80) cc_final: 0.7517 (m-80) REVERT: V1 415 GLU cc_start: 0.8212 (mp0) cc_final: 0.7855 (mp0) REVERT: V1 435 GLU cc_start: 0.8773 (mp0) cc_final: 0.8191 (mp0) REVERT: V2 78 GLN cc_start: 0.8996 (mt0) cc_final: 0.8513 (mt0) REVERT: 1M 57 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (tttp) REVERT: 1M 102 ASP cc_start: 0.8486 (t0) cc_final: 0.8152 (t0) REVERT: 1M 178 TRP cc_start: 0.9297 (m-10) cc_final: 0.8707 (m-10) REVERT: 1M 198 THR cc_start: 0.9040 (p) cc_final: 0.8600 (p) REVERT: 1M 199 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7025 (m-40) REVERT: 1M 262 ARG cc_start: 0.8270 (tpt170) cc_final: 0.7944 (mtt180) REVERT: 2M 113 GLU cc_start: 0.8397 (mp0) cc_final: 0.8076 (mp0) REVERT: 2M 179 LEU cc_start: 0.9539 (tp) cc_final: 0.9306 (tt) REVERT: 2M 243 TYR cc_start: 0.7852 (m-10) cc_final: 0.7497 (m-10) REVERT: 2M 244 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8348 (tm-30) REVERT: 2M 299 MET cc_start: 0.8264 (tmm) cc_final: 0.7885 (tmm) REVERT: 2M 347 ASP cc_start: 0.8725 (t70) cc_final: 0.8392 (t0) REVERT: 2M 434 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6748 (tmtt) REVERT: 2M 436 MET cc_start: 0.7851 (mmm) cc_final: 0.6427 (ppp) REVERT: 3M 115 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8958 (pp) REVERT: 4L 6 TYR cc_start: 0.8941 (m-80) cc_final: 0.8611 (m-80) REVERT: 4L 33 MET cc_start: 0.7984 (mtm) cc_final: 0.7715 (mtp) REVERT: 4L 77 LEU cc_start: 0.9086 (tp) cc_final: 0.8808 (tp) REVERT: A1 4 ARG cc_start: 0.8773 (tpp-160) cc_final: 0.8459 (tpp-160) REVERT: A1 49 MET cc_start: 0.8583 (mmp) cc_final: 0.8054 (mmm) REVERT: A1 52 ARG cc_start: 0.8633 (ttt-90) cc_final: 0.8260 (ttt90) REVERT: A8 45 ASN cc_start: 0.8850 (t0) cc_final: 0.8116 (t0) REVERT: A8 74 GLU cc_start: 0.8820 (mp0) cc_final: 0.8396 (mt-10) REVERT: AM 18 MET cc_start: 0.6670 (ptt) cc_final: 0.5370 (ptt) REVERT: AM 85 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8876 (tp) REVERT: C2 26 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9188 (pp) REVERT: P2 105 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8174 (mmmm) REVERT: S5 11 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8402 (ttmm) REVERT: S5 27 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7716 (ttp80) REVERT: S5 30 GLU cc_start: 0.6563 (tp30) cc_final: 0.6199 (mm-30) REVERT: S5 49 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8310 (ttpt) REVERT: X1 10 LYS cc_start: 0.8641 (mttt) cc_final: 0.8399 (mttp) REVERT: G1 16 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8684 (ttp-170) REVERT: G1 38 GLN cc_start: 0.9075 (mp10) cc_final: 0.8861 (mp10) REVERT: G1 80 TRP cc_start: 0.9194 (m100) cc_final: 0.8785 (m100) REVERT: G1 102 ASP cc_start: 0.8793 (p0) cc_final: 0.8573 (p0) REVERT: G1 128 VAL cc_start: 0.9358 (t) cc_final: 0.9026 (p) REVERT: G1 206 ASN cc_start: 0.8496 (m-40) cc_final: 0.8195 (m-40) REVERT: G2 86 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8705 (ttp80) REVERT: G2 101 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8204 (mm-40) REVERT: G2 140 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: G2 155 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8293 (p) REVERT: L2 83 VAL cc_start: 0.9370 (t) cc_final: 0.9078 (p) REVERT: L2 165 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8246 (m170) REVERT: L2 181 GLU cc_start: 0.8250 (tt0) cc_final: 0.8048 (tt0) REVERT: L2 235 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8322 (t80) REVERT: L2 246 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7663 (tm-30) outliers start: 211 outliers final: 133 residues processed: 1472 average time/residue: 0.2400 time to fit residues: 587.2912 Evaluate side-chains 1377 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1233 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A7 residue 84 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 153 VAL Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 53 VAL Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 169 LEU Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 324 ILE Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S1 residue 692 ASP Chi-restraints excluded: chain S1 residue 725 MET Chi-restraints excluded: chain S2 residue 148 VAL Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 6 ILE Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 121 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S6 residue 58 VAL Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 142 VAL Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 270 VAL Chi-restraints excluded: chain V1 residue 434 LEU Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain 1M residue 57 LYS Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 105 ILE Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 161 CYS Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 199 ASN Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 266 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 4L residue 37 LEU Chi-restraints excluded: chain 4L residue 51 VAL Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 139 THR Chi-restraints excluded: chain 6M residue 143 LEU Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A8 residue 60 VAL Chi-restraints excluded: chain A8 residue 64 LEU Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 49 ILE Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 7 THR Chi-restraints excluded: chain C2 residue 20 SER Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 14 CYS Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain X1 residue 85 LEU Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 140 GLU Chi-restraints excluded: chain G2 residue 155 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 196 GLU Chi-restraints excluded: chain G2 residue 213 VAL Chi-restraints excluded: chain L2 residue 46 THR Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 235 PHE Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 375 optimal weight: 0.7980 chunk 304 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 395 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 502 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 424 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 397 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A6 130 ASN A9 133 ASN AL 137 HIS S1 557 HIS ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 640 GLN S1 683 ASN S2 280 ASN S2 364 GLN ** S7 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1M 143 GLN 1M 199 ASN ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 209 ASN G1 212 GLN G2 218 ASN L2 81 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106901 restraints weight = 67693.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109751 restraints weight = 39503.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111649 restraints weight = 27811.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.112807 restraints weight = 22022.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.113713 restraints weight = 18912.573| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.249 46100 Z= 0.341 Angle : 2.121 61.332 62544 Z= 1.242 Chirality : 0.372 6.347 6946 Planarity : 0.005 0.090 7932 Dihedral : 7.292 88.774 6481 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.30 % Favored : 89.59 % Rotamer: Outliers : 4.72 % Allowed : 22.17 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.11), residues: 5572 helix: 1.20 (0.10), residues: 2697 sheet: -1.62 (0.26), residues: 412 loop : -3.03 (0.11), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGV1 330 TYR 0.070 0.002 TYR2M 149 PHE 0.038 0.001 PHEA9 371 TRP 0.034 0.001 TRPA5 109 HIS 0.013 0.001 HIS2M 69 Details of bonding type rmsd covalent geometry : bond 0.00983 (46061) covalent geometry : angle 1.91377 (62467) SS BOND : bond 0.00608 ( 7) SS BOND : angle 3.38203 ( 14) hydrogen bonds : bond 0.04731 ( 2233) hydrogen bonds : angle 5.04936 ( 6492) metal coordination : bond 0.02099 ( 32) metal coordination : angle 28.86549 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1299 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A5 88 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A6 124 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8591 (tttp) REVERT: A7 52 GLU cc_start: 0.7353 (mp0) cc_final: 0.6935 (mp0) REVERT: A7 57 PRO cc_start: 0.8953 (Cg_exo) cc_final: 0.8659 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7868 (tm-30) REVERT: A7 109 TYR cc_start: 0.8921 (t80) cc_final: 0.8119 (t80) REVERT: A9 222 ARG cc_start: 0.8416 (mpp80) cc_final: 0.7919 (mtt180) REVERT: A9 265 ASP cc_start: 0.6552 (m-30) cc_final: 0.6242 (m-30) REVERT: A9 298 TRP cc_start: 0.6047 (m100) cc_final: 0.4732 (m-10) REVERT: AL 45 ASN cc_start: 0.8457 (m-40) cc_final: 0.8186 (m-40) REVERT: AL 77 TYR cc_start: 0.8866 (m-80) cc_final: 0.8510 (m-80) REVERT: S1 117 ASN cc_start: 0.8314 (t0) cc_final: 0.7905 (t0) REVERT: S1 124 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: S1 165 MET cc_start: 0.8648 (tmm) cc_final: 0.8235 (ttt) REVERT: S1 231 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7995 (mt-10) REVERT: S1 371 ASP cc_start: 0.7775 (t0) cc_final: 0.7524 (t70) REVERT: S1 461 LYS cc_start: 0.9003 (tptm) cc_final: 0.8579 (tttm) REVERT: S1 556 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8408 (pp) REVERT: S1 604 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8678 (tm-30) REVERT: S1 690 ASN cc_start: 0.8889 (t0) cc_final: 0.8134 (t0) REVERT: S2 76 MET cc_start: 0.8960 (mtt) cc_final: 0.8673 (ttm) REVERT: S2 87 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8488 (mt-10) REVERT: S2 143 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8539 (tm-30) REVERT: S2 166 ASP cc_start: 0.8656 (t70) cc_final: 0.8192 (t0) REVERT: S2 201 GLN cc_start: 0.8958 (tt0) cc_final: 0.8701 (tt0) REVERT: S2 212 GLN cc_start: 0.8635 (tp40) cc_final: 0.8117 (tp40) REVERT: S2 223 MET cc_start: 0.9314 (mmm) cc_final: 0.9084 (mmm) REVERT: S3 1 MET cc_start: 0.7646 (tmm) cc_final: 0.7142 (tmm) REVERT: S3 84 SER cc_start: 0.9055 (m) cc_final: 0.8753 (t) REVERT: S3 91 SER cc_start: 0.9348 (t) cc_final: 0.8958 (p) REVERT: S3 167 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6973 (mt-10) REVERT: S6 39 GLN cc_start: 0.8662 (tp40) cc_final: 0.8382 (tp40) REVERT: S8 49 ARG cc_start: 0.8663 (ttm170) cc_final: 0.7032 (tpt170) REVERT: S8 59 ASP cc_start: 0.8447 (p0) cc_final: 0.8022 (p0) REVERT: S8 208 GLU cc_start: 0.8851 (tp30) cc_final: 0.8552 (tp30) REVERT: S8 213 GLU cc_start: 0.8724 (tp30) cc_final: 0.8362 (tp30) REVERT: V1 68 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8335 (mtt90) REVERT: V1 162 ASP cc_start: 0.8397 (t0) cc_final: 0.8126 (t70) REVERT: V1 165 LYS cc_start: 0.8750 (tppt) cc_final: 0.8528 (mmtm) REVERT: V1 190 TYR cc_start: 0.8663 (m-80) cc_final: 0.8210 (m-80) REVERT: V1 268 THR cc_start: 0.8760 (p) cc_final: 0.8506 (p) REVERT: V1 297 ASN cc_start: 0.8671 (m110) cc_final: 0.8162 (t0) REVERT: V1 367 TYR cc_start: 0.7983 (m-80) cc_final: 0.7438 (m-80) REVERT: V1 390 ASP cc_start: 0.7997 (m-30) cc_final: 0.7653 (m-30) REVERT: V1 415 GLU cc_start: 0.8190 (mp0) cc_final: 0.7868 (mp0) REVERT: V1 435 GLU cc_start: 0.8746 (mp0) cc_final: 0.8172 (mp0) REVERT: 1M 102 ASP cc_start: 0.8460 (t0) cc_final: 0.8124 (t0) REVERT: 1M 178 TRP cc_start: 0.9288 (m-10) cc_final: 0.8723 (m-10) REVERT: 1M 198 THR cc_start: 0.9009 (p) cc_final: 0.8524 (p) REVERT: 1M 262 ARG cc_start: 0.8267 (tpt170) cc_final: 0.7937 (mtt180) REVERT: 1M 280 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8160 (t80) REVERT: 2M 105 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8023 (tp30) REVERT: 2M 179 LEU cc_start: 0.9497 (tp) cc_final: 0.9294 (tt) REVERT: 2M 243 TYR cc_start: 0.7880 (m-10) cc_final: 0.7536 (m-80) REVERT: 2M 244 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8322 (tm-30) REVERT: 2M 265 ASN cc_start: 0.9268 (t160) cc_final: 0.9053 (t0) REVERT: 2M 347 ASP cc_start: 0.8730 (t70) cc_final: 0.8370 (t0) REVERT: 2M 434 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6717 (tmtt) REVERT: 2M 436 MET cc_start: 0.8000 (mmm) cc_final: 0.6373 (ppp) REVERT: 3M 96 MET cc_start: 0.8780 (mmp) cc_final: 0.8273 (mmt) REVERT: 3M 115 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8932 (pp) REVERT: 4L 6 TYR cc_start: 0.8955 (m-80) cc_final: 0.8565 (m-80) REVERT: 6M 32 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9107 (tt) REVERT: 6M 70 MET cc_start: 0.9150 (mmp) cc_final: 0.8598 (mmt) REVERT: A1 4 ARG cc_start: 0.8732 (tpp-160) cc_final: 0.8430 (tpp-160) REVERT: A1 49 MET cc_start: 0.8601 (mmp) cc_final: 0.7975 (mmm) REVERT: A1 53 ASP cc_start: 0.8783 (m-30) cc_final: 0.8564 (m-30) REVERT: A8 45 ASN cc_start: 0.8837 (t0) cc_final: 0.8134 (t0) REVERT: A8 74 GLU cc_start: 0.8833 (mp0) cc_final: 0.8373 (mt-10) REVERT: AM 85 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8825 (tp) REVERT: AM 112 MET cc_start: 0.7865 (mmm) cc_final: 0.7593 (mmm) REVERT: C2 26 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9188 (pp) REVERT: S5 11 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8484 (ttmm) REVERT: S5 49 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8308 (ttpt) REVERT: X1 10 LYS cc_start: 0.8650 (mttt) cc_final: 0.8278 (mttp) REVERT: X1 29 PHE cc_start: 0.9047 (m-10) cc_final: 0.8752 (m-10) REVERT: G1 80 TRP cc_start: 0.9131 (m100) cc_final: 0.8672 (m100) REVERT: G1 102 ASP cc_start: 0.8832 (p0) cc_final: 0.8589 (p0) REVERT: G1 128 VAL cc_start: 0.9431 (t) cc_final: 0.9148 (p) REVERT: G1 138 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8028 (p) REVERT: G2 207 TYR cc_start: 0.8056 (t80) cc_final: 0.7475 (t80) REVERT: L2 165 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8215 (m170) REVERT: L2 235 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8388 (t80) REVERT: L2 246 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7678 (tm-30) outliers start: 224 outliers final: 151 residues processed: 1438 average time/residue: 0.2259 time to fit residues: 541.8955 Evaluate side-chains 1379 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1218 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A7 residue 84 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 153 VAL Chi-restraints excluded: chain A9 residue 290 LEU Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 169 LEU Chi-restraints excluded: chain S1 residue 215 VAL Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 292 GLU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S1 residue 692 ASP Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 162 LYS Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S6 residue 58 VAL Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 177 ILE Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 141 LEU Chi-restraints excluded: chain V1 residue 142 VAL Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 222 ASP Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 434 LEU Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V2 residue 33 ASP Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain 1M residue 89 TRP Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 199 ASN Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 1M residue 254 ILE Chi-restraints excluded: chain 1M residue 280 TYR Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 266 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 465 ILE Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 82 VAL Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 37 LEU Chi-restraints excluded: chain 4L residue 51 VAL Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 4L residue 72 GLU Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 121 SER Chi-restraints excluded: chain 6M residue 143 LEU Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A8 residue 60 VAL Chi-restraints excluded: chain A8 residue 64 LEU Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 49 ILE Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 20 SER Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 14 CYS Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 53 ILE Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain X1 residue 85 LEU Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 88 ASP Chi-restraints excluded: chain G1 residue 138 THR Chi-restraints excluded: chain G1 residue 202 GLN Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain L2 residue 46 THR Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 235 PHE Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 151 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 541 optimal weight: 3.9990 chunk 358 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 334 optimal weight: 0.4980 chunk 497 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 478 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A9 80 GLN AL 137 HIS ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 385 GLN S7 161 HIS ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1M 199 ASN ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 69 HIS 2M 481 GLN ** 6M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 218 ASN G2 218 ASN L2 81 ASN ** L2 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.108110 restraints weight = 68006.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110907 restraints weight = 40029.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.112793 restraints weight = 28341.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.114045 restraints weight = 22498.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114901 restraints weight = 19240.034| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.251 46100 Z= 0.342 Angle : 2.124 59.302 62544 Z= 1.243 Chirality : 0.372 6.345 6946 Planarity : 0.005 0.089 7932 Dihedral : 7.146 89.755 6481 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.07 % Favored : 89.84 % Rotamer: Outliers : 4.70 % Allowed : 22.97 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.11), residues: 5572 helix: 1.28 (0.10), residues: 2699 sheet: -1.63 (0.26), residues: 417 loop : -2.91 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGV1 330 TYR 0.076 0.002 TYR2M 149 PHE 0.036 0.001 PHEA9 306 TRP 0.025 0.001 TRPA5 109 HIS 0.012 0.001 HIS2M 69 Details of bonding type rmsd covalent geometry : bond 0.00985 (46061) covalent geometry : angle 1.91652 (62467) SS BOND : bond 0.00558 ( 7) SS BOND : angle 3.00156 ( 14) hydrogen bonds : bond 0.04630 ( 2233) hydrogen bonds : angle 4.99747 ( 6492) metal coordination : bond 0.01957 ( 32) metal coordination : angle 28.91731 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1489 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 1266 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 73 LYS cc_start: 0.8282 (mptt) cc_final: 0.8043 (mmtt) REVERT: A5 80 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8488 (ttm170) REVERT: A5 88 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A6 124 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8598 (tttp) REVERT: A7 52 GLU cc_start: 0.7344 (mp0) cc_final: 0.6927 (mp0) REVERT: A7 92 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7903 (tm-30) REVERT: A7 109 TYR cc_start: 0.8900 (t80) cc_final: 0.8109 (t80) REVERT: A9 222 ARG cc_start: 0.8445 (mpp80) cc_final: 0.7933 (mtt180) REVERT: A9 265 ASP cc_start: 0.6706 (m-30) cc_final: 0.6414 (m-30) REVERT: A9 298 TRP cc_start: 0.6206 (m100) cc_final: 0.4906 (m-10) REVERT: A9 306 PHE cc_start: 0.7530 (p90) cc_final: 0.6940 (m-80) REVERT: AL 45 ASN cc_start: 0.8542 (m-40) cc_final: 0.8296 (m-40) REVERT: AL 77 TYR cc_start: 0.8863 (m-80) cc_final: 0.8507 (m-80) REVERT: AL 134 SER cc_start: 0.8931 (p) cc_final: 0.8696 (t) REVERT: S1 117 ASN cc_start: 0.8259 (t0) cc_final: 0.7835 (t0) REVERT: S1 124 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: S1 165 MET cc_start: 0.8610 (tmm) cc_final: 0.8221 (ttt) REVERT: S1 231 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8014 (mt-10) REVERT: S1 461 LYS cc_start: 0.9003 (tptm) cc_final: 0.8755 (tttm) REVERT: S1 556 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8424 (pp) REVERT: S1 604 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8656 (tm-30) REVERT: S2 87 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8471 (mt-10) REVERT: S2 143 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8529 (tm-30) REVERT: S2 166 ASP cc_start: 0.8712 (t70) cc_final: 0.8223 (t0) REVERT: S2 212 GLN cc_start: 0.8625 (tp40) cc_final: 0.8135 (tp40) REVERT: S2 223 MET cc_start: 0.9286 (mmm) cc_final: 0.9082 (mmm) REVERT: S2 248 ASP cc_start: 0.7971 (m-30) cc_final: 0.7635 (t0) REVERT: S3 1 MET cc_start: 0.7770 (tmm) cc_final: 0.7239 (tmm) REVERT: S3 84 SER cc_start: 0.9060 (m) cc_final: 0.8737 (t) REVERT: S3 91 SER cc_start: 0.9336 (t) cc_final: 0.8937 (p) REVERT: S3 167 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6985 (mt-10) REVERT: S6 39 GLN cc_start: 0.8663 (tp40) cc_final: 0.8415 (tt0) REVERT: S8 49 ARG cc_start: 0.8654 (ttm170) cc_final: 0.7050 (tpt170) REVERT: S8 59 ASP cc_start: 0.8408 (p0) cc_final: 0.8016 (p0) REVERT: S8 208 GLU cc_start: 0.8810 (tp30) cc_final: 0.8493 (tp30) REVERT: S8 213 GLU cc_start: 0.8690 (tp30) cc_final: 0.8317 (tp30) REVERT: V1 68 ARG cc_start: 0.8618 (mtt90) cc_final: 0.8259 (mtt90) REVERT: V1 190 TYR cc_start: 0.8607 (m-80) cc_final: 0.8297 (m-80) REVERT: V1 202 GLN cc_start: 0.8955 (tp40) cc_final: 0.8752 (tp40) REVERT: V1 268 THR cc_start: 0.8693 (p) cc_final: 0.8439 (p) REVERT: V1 297 ASN cc_start: 0.8632 (m110) cc_final: 0.8142 (t0) REVERT: V1 325 LYS cc_start: 0.8574 (tttp) cc_final: 0.8291 (tttt) REVERT: V1 390 ASP cc_start: 0.8002 (m-30) cc_final: 0.7659 (m-30) REVERT: V1 435 GLU cc_start: 0.8700 (mp0) cc_final: 0.8133 (mp0) REVERT: 1M 57 LYS cc_start: 0.8858 (tttm) cc_final: 0.8461 (tttp) REVERT: 1M 102 ASP cc_start: 0.8444 (t0) cc_final: 0.8066 (t0) REVERT: 1M 198 THR cc_start: 0.8891 (p) cc_final: 0.8501 (p) REVERT: 1M 262 ARG cc_start: 0.8217 (tpt170) cc_final: 0.7931 (mtt180) REVERT: 1M 280 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8138 (t80) REVERT: 1M 302 VAL cc_start: 0.9635 (t) cc_final: 0.9421 (p) REVERT: 2M 105 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8044 (tp30) REVERT: 2M 162 THR cc_start: 0.5849 (OUTLIER) cc_final: 0.5535 (m) REVERT: 2M 243 TYR cc_start: 0.7905 (m-10) cc_final: 0.7592 (m-10) REVERT: 2M 244 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8321 (tm-30) REVERT: 2M 265 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.9091 (t0) REVERT: 2M 434 LYS cc_start: 0.7150 (mmtm) cc_final: 0.6681 (tmtt) REVERT: 2M 436 MET cc_start: 0.7980 (mmm) cc_final: 0.6370 (ppp) REVERT: 3M 96 MET cc_start: 0.8749 (mmp) cc_final: 0.8261 (mmt) REVERT: 3M 115 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8946 (pp) REVERT: 4L 6 TYR cc_start: 0.8938 (m-80) cc_final: 0.8547 (m-80) REVERT: 6M 32 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9117 (tt) REVERT: 6M 70 MET cc_start: 0.9131 (mmp) cc_final: 0.8499 (mmt) REVERT: A1 4 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8381 (tpp-160) REVERT: A1 36 ARG cc_start: 0.9024 (ptp-170) cc_final: 0.8737 (ptt180) REVERT: A1 49 MET cc_start: 0.8554 (mmp) cc_final: 0.7984 (mmm) REVERT: A1 52 ARG cc_start: 0.8439 (ttt-90) cc_final: 0.8103 (ttt90) REVERT: A1 53 ASP cc_start: 0.8798 (m-30) cc_final: 0.8598 (m-30) REVERT: A8 45 ASN cc_start: 0.8806 (t0) cc_final: 0.8047 (t0) REVERT: A8 74 GLU cc_start: 0.8814 (mp0) cc_final: 0.8268 (mt-10) REVERT: A8 94 LYS cc_start: 0.8921 (tptp) cc_final: 0.8366 (mmtp) REVERT: AM 85 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8794 (tp) REVERT: AM 112 MET cc_start: 0.7924 (mmm) cc_final: 0.7547 (mmm) REVERT: C2 21 ASN cc_start: 0.8814 (m-40) cc_final: 0.8461 (t0) REVERT: C2 26 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.8974 (pp) REVERT: S5 11 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8422 (ttmm) REVERT: S5 27 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7618 (ttp80) REVERT: X1 10 LYS cc_start: 0.8627 (mttt) cc_final: 0.8377 (mttp) REVERT: X1 29 PHE cc_start: 0.8985 (m-10) cc_final: 0.8696 (m-10) REVERT: G1 80 TRP cc_start: 0.9074 (m100) cc_final: 0.8646 (m100) REVERT: G1 102 ASP cc_start: 0.8840 (p0) cc_final: 0.8583 (p0) REVERT: G1 128 VAL cc_start: 0.9438 (t) cc_final: 0.9211 (p) REVERT: G1 138 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8018 (p) REVERT: L2 71 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8753 (ttmt) REVERT: L2 75 ASP cc_start: 0.8776 (t70) cc_final: 0.8564 (t0) REVERT: L2 165 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8079 (m170) REVERT: L2 235 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8384 (t80) outliers start: 223 outliers final: 159 residues processed: 1401 average time/residue: 0.2034 time to fit residues: 477.2180 Evaluate side-chains 1386 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1215 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 64 ILE Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 216 MET Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 332 ILE Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 169 LEU Chi-restraints excluded: chain S1 residue 174 CYS Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 162 LYS Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 112 HIS Chi-restraints excluded: chain S6 residue 58 VAL Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 171 ASP Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 177 ILE Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 158 ILE Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 270 VAL Chi-restraints excluded: chain V1 residue 434 LEU Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 33 ASP Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain V2 residue 235 THR Chi-restraints excluded: chain V2 residue 236 LEU Chi-restraints excluded: chain 1M residue 64 ILE Chi-restraints excluded: chain 1M residue 89 TRP Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 119 TYR Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 1M residue 254 ILE Chi-restraints excluded: chain 1M residue 280 TYR Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 265 ASN Chi-restraints excluded: chain 2M residue 266 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 343 LEU Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 435 ARG Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 82 VAL Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 37 LEU Chi-restraints excluded: chain 4L residue 51 VAL Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 4L residue 72 GLU Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 143 LEU Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A1 residue 15 ILE Chi-restraints excluded: chain A3 residue 33 VAL Chi-restraints excluded: chain A8 residue 60 VAL Chi-restraints excluded: chain A8 residue 64 LEU Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 49 ILE Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 14 CYS Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain X1 residue 85 LEU Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 138 THR Chi-restraints excluded: chain G1 residue 153 ASP Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 94 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 218 ASN Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 88 VAL Chi-restraints excluded: chain L2 residue 92 ASP Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 194 SER Chi-restraints excluded: chain L2 residue 235 PHE Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 537 optimal weight: 2.9990 chunk 440 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 553 optimal weight: 4.9990 chunk 441 optimal weight: 2.9990 chunk 514 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AL 137 HIS ** S1 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 126 HIS S7 202 ASN ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 36 GLN G2 218 ASN L2 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.122221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.102213 restraints weight = 66470.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.104738 restraints weight = 43565.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.106381 restraints weight = 31421.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.107422 restraints weight = 23664.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.107857 restraints weight = 20639.940| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.242 46100 Z= 0.370 Angle : 2.154 59.176 62544 Z= 1.252 Chirality : 0.373 6.368 6946 Planarity : 0.005 0.093 7932 Dihedral : 7.257 88.088 6481 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.27 % Rotamer: Outliers : 4.95 % Allowed : 23.75 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.11), residues: 5572 helix: 1.23 (0.10), residues: 2703 sheet: -1.41 (0.26), residues: 431 loop : -2.91 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGV1 330 TYR 0.067 0.002 TYR2M 149 PHE 0.029 0.002 PHEA3 26 TRP 0.028 0.001 TRPA5 109 HIS 0.007 0.001 HISS2 80 Details of bonding type rmsd covalent geometry : bond 0.01037 (46061) covalent geometry : angle 1.93682 (62467) SS BOND : bond 0.00517 ( 7) SS BOND : angle 2.41945 ( 14) hydrogen bonds : bond 0.05305 ( 2233) hydrogen bonds : angle 5.13819 ( 6492) metal coordination : bond 0.02275 ( 32) metal coordination : angle 29.73039 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 1246 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 38 GLU cc_start: 0.7238 (pt0) cc_final: 0.6958 (tt0) REVERT: A2 73 LYS cc_start: 0.8316 (mptt) cc_final: 0.8057 (mmtt) REVERT: A2 79 GLU cc_start: 0.8233 (tp30) cc_final: 0.8020 (tp30) REVERT: A2 82 ILE cc_start: 0.8947 (tt) cc_final: 0.8730 (tp) REVERT: A5 88 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7434 (tm-30) REVERT: A7 52 GLU cc_start: 0.7481 (mp0) cc_final: 0.7132 (mp0) REVERT: A7 57 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8603 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7917 (tm-30) REVERT: A7 109 TYR cc_start: 0.8912 (t80) cc_final: 0.8148 (t80) REVERT: A9 222 ARG cc_start: 0.8474 (mpp80) cc_final: 0.8120 (mtt180) REVERT: A9 298 TRP cc_start: 0.6236 (m100) cc_final: 0.5107 (m-10) REVERT: A9 306 PHE cc_start: 0.7558 (p90) cc_final: 0.6943 (m-10) REVERT: AL 45 ASN cc_start: 0.8522 (m-40) cc_final: 0.8264 (m-40) REVERT: AL 77 TYR cc_start: 0.8948 (m-80) cc_final: 0.8544 (m-80) REVERT: AL 134 SER cc_start: 0.9060 (p) cc_final: 0.8846 (t) REVERT: S1 117 ASN cc_start: 0.8291 (t0) cc_final: 0.7908 (t0) REVERT: S1 124 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: S1 165 MET cc_start: 0.8662 (tmm) cc_final: 0.8439 (ttp) REVERT: S1 221 GLN cc_start: 0.8277 (mp10) cc_final: 0.8062 (mp10) REVERT: S1 231 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7879 (mt-10) REVERT: S1 461 LYS cc_start: 0.9050 (tptm) cc_final: 0.8610 (tttm) REVERT: S1 556 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8366 (pp) REVERT: S1 604 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8565 (tm-30) REVERT: S2 87 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8617 (mt-10) REVERT: S2 166 ASP cc_start: 0.8708 (t70) cc_final: 0.8305 (t0) REVERT: S2 201 GLN cc_start: 0.8859 (tt0) cc_final: 0.8653 (tt0) REVERT: S2 212 GLN cc_start: 0.8656 (tp40) cc_final: 0.8173 (tp40) REVERT: S3 1 MET cc_start: 0.7681 (tmm) cc_final: 0.7234 (tmm) REVERT: S3 84 SER cc_start: 0.9045 (m) cc_final: 0.8724 (t) REVERT: S4 135 PHE cc_start: 0.8257 (m-80) cc_final: 0.7949 (m-10) REVERT: S8 49 ARG cc_start: 0.8695 (ttm170) cc_final: 0.7215 (tpt170) REVERT: S8 59 ASP cc_start: 0.8418 (p0) cc_final: 0.8217 (p0) REVERT: S8 195 TYR cc_start: 0.8610 (m-80) cc_final: 0.8252 (m-80) REVERT: S8 213 GLU cc_start: 0.8737 (tp30) cc_final: 0.8354 (tp30) REVERT: V1 132 LYS cc_start: 0.8480 (ptpt) cc_final: 0.7927 (tptm) REVERT: V1 144 ASN cc_start: 0.9313 (t0) cc_final: 0.8862 (t0) REVERT: V1 190 TYR cc_start: 0.8704 (m-80) cc_final: 0.8333 (m-80) REVERT: V1 268 THR cc_start: 0.8693 (p) cc_final: 0.8469 (p) REVERT: V1 297 ASN cc_start: 0.8543 (m110) cc_final: 0.8103 (t0) REVERT: V1 435 GLU cc_start: 0.8772 (mp0) cc_final: 0.8218 (mp0) REVERT: 1M 57 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8533 (tttp) REVERT: 1M 102 ASP cc_start: 0.8370 (t0) cc_final: 0.8063 (t0) REVERT: 1M 198 THR cc_start: 0.9195 (p) cc_final: 0.8651 (p) REVERT: 1M 280 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8208 (t80) REVERT: 2M 105 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7978 (tp30) REVERT: 2M 243 TYR cc_start: 0.7944 (m-80) cc_final: 0.7703 (m-80) REVERT: 2M 244 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8402 (tm-30) REVERT: 2M 434 LYS cc_start: 0.7434 (mmtm) cc_final: 0.7067 (tmtt) REVERT: 2M 436 MET cc_start: 0.7920 (mmm) cc_final: 0.6542 (tmm) REVERT: 3M 96 MET cc_start: 0.8674 (mmp) cc_final: 0.8286 (mmt) REVERT: 3M 115 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8966 (pp) REVERT: 4L 6 TYR cc_start: 0.8857 (m-80) cc_final: 0.8479 (m-80) REVERT: 6M 70 MET cc_start: 0.9090 (mmp) cc_final: 0.8538 (mmt) REVERT: A1 4 ARG cc_start: 0.8668 (tpp-160) cc_final: 0.8410 (tpp-160) REVERT: A1 52 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8166 (ttt90) REVERT: A1 53 ASP cc_start: 0.8769 (m-30) cc_final: 0.8502 (m-30) REVERT: A8 19 MET cc_start: 0.8765 (mmm) cc_final: 0.8386 (mtp) REVERT: A8 45 ASN cc_start: 0.8742 (t0) cc_final: 0.8059 (t0) REVERT: A8 74 GLU cc_start: 0.8656 (mp0) cc_final: 0.8180 (mt-10) REVERT: AM 85 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8935 (tp) REVERT: C2 26 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9261 (pp) REVERT: P2 105 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8153 (mmmm) REVERT: X1 10 LYS cc_start: 0.8609 (mttt) cc_final: 0.8284 (ttmm) REVERT: G1 23 ASP cc_start: 0.8281 (t0) cc_final: 0.7560 (t0) REVERT: G1 80 TRP cc_start: 0.9126 (m100) cc_final: 0.8717 (m100) REVERT: G1 128 VAL cc_start: 0.9420 (t) cc_final: 0.9174 (p) REVERT: G1 138 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8208 (p) REVERT: L2 103 ARG cc_start: 0.8745 (ttp80) cc_final: 0.7973 (ttp80) REVERT: L2 165 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8226 (m170) outliers start: 235 outliers final: 174 residues processed: 1389 average time/residue: 0.1884 time to fit residues: 438.3005 Evaluate side-chains 1399 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1216 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A2 residue 88 ASP Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 64 ILE Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 153 VAL Chi-restraints excluded: chain A9 residue 216 MET Chi-restraints excluded: chain A9 residue 290 LEU Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 332 ILE Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 59 SER Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 174 CYS Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 496 ILE Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 310 ILE Chi-restraints excluded: chain S2 residue 387 ILE Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 162 LYS Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 70 LEU Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 167 VAL Chi-restraints excluded: chain S7 residue 171 ASP Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 141 LEU Chi-restraints excluded: chain V1 residue 158 ILE Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 222 ASP Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 270 VAL Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain V2 residue 235 THR Chi-restraints excluded: chain 1M residue 57 LYS Chi-restraints excluded: chain 1M residue 64 ILE Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 119 TYR Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 1M residue 248 LEU Chi-restraints excluded: chain 1M residue 276 PHE Chi-restraints excluded: chain 1M residue 280 TYR Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 266 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 343 LEU Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 435 ARG Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 456 LEU Chi-restraints excluded: chain 2M residue 465 ILE Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 64 SER Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 103 THR Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 46 PHE Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 4L residue 72 GLU Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 135 THR Chi-restraints excluded: chain 6M residue 143 LEU Chi-restraints excluded: chain 6M residue 146 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A1 residue 40 ILE Chi-restraints excluded: chain A3 residue 33 VAL Chi-restraints excluded: chain A8 residue 60 VAL Chi-restraints excluded: chain A8 residue 64 LEU Chi-restraints excluded: chain A8 residue 66 ASP Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 7 THR Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 53 ILE Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain X1 residue 85 LEU Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 32 ASN Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 73 VAL Chi-restraints excluded: chain G1 residue 88 ASP Chi-restraints excluded: chain G1 residue 138 THR Chi-restraints excluded: chain G1 residue 153 ASP Chi-restraints excluded: chain G1 residue 197 MET Chi-restraints excluded: chain G1 residue 202 GLN Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 94 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 168 LEU Chi-restraints excluded: chain G2 residue 173 THR Chi-restraints excluded: chain G2 residue 200 ILE Chi-restraints excluded: chain G2 residue 230 VAL Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 88 VAL Chi-restraints excluded: chain L2 residue 105 ASP Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 194 SER Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 344 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 360 optimal weight: 0.7980 chunk 337 optimal weight: 9.9990 chunk 239 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 468 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 403 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A9 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 375 GLN ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 62 GLN V1 331 HIS V1 446 GLN ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 236 HIS 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6M 136 ASN ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 36 GLN G2 218 ASN L2 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.106666 restraints weight = 66317.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.109243 restraints weight = 43121.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.110923 restraints weight = 30727.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.112293 restraints weight = 23194.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.112515 restraints weight = 19510.912| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.249 46100 Z= 0.346 Angle : 2.141 58.638 62544 Z= 1.247 Chirality : 0.372 6.350 6946 Planarity : 0.005 0.089 7932 Dihedral : 7.123 88.040 6481 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.23 % Favored : 89.70 % Rotamer: Outliers : 4.40 % Allowed : 25.08 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 5572 helix: 1.29 (0.10), residues: 2700 sheet: -1.42 (0.27), residues: 422 loop : -2.79 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGV1 330 TYR 0.063 0.002 TYR2M 149 PHE 0.029 0.001 PHEA9 371 TRP 0.030 0.001 TRPA5 109 HIS 0.009 0.001 HISV1 331 Details of bonding type rmsd covalent geometry : bond 0.00992 (46061) covalent geometry : angle 1.92767 (62467) SS BOND : bond 0.00450 ( 7) SS BOND : angle 1.87774 ( 14) hydrogen bonds : bond 0.04803 ( 2233) hydrogen bonds : angle 5.04124 ( 6492) metal coordination : bond 0.01847 ( 32) metal coordination : angle 29.40994 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1251 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 38 GLU cc_start: 0.7196 (pt0) cc_final: 0.6931 (tt0) REVERT: A2 73 LYS cc_start: 0.8295 (mptt) cc_final: 0.8069 (mmtt) REVERT: A2 79 GLU cc_start: 0.8204 (tp30) cc_final: 0.7994 (tp30) REVERT: A2 82 ILE cc_start: 0.8851 (tt) cc_final: 0.8612 (tp) REVERT: A5 80 ARG cc_start: 0.8787 (ttm-80) cc_final: 0.8410 (ttm170) REVERT: A5 88 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A7 52 GLU cc_start: 0.7433 (mp0) cc_final: 0.7004 (mp0) REVERT: A7 92 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7904 (tm-30) REVERT: A7 109 TYR cc_start: 0.8838 (t80) cc_final: 0.7953 (t80) REVERT: A9 222 ARG cc_start: 0.8457 (mpp80) cc_final: 0.8094 (mtt180) REVERT: A9 298 TRP cc_start: 0.6185 (m100) cc_final: 0.5188 (m-10) REVERT: A9 306 PHE cc_start: 0.7544 (p90) cc_final: 0.6944 (m-10) REVERT: AL 45 ASN cc_start: 0.8487 (m-40) cc_final: 0.8268 (m-40) REVERT: AL 77 TYR cc_start: 0.8845 (m-80) cc_final: 0.8550 (m-80) REVERT: AL 134 SER cc_start: 0.8994 (p) cc_final: 0.8778 (t) REVERT: S1 117 ASN cc_start: 0.8228 (t0) cc_final: 0.7815 (t0) REVERT: S1 124 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: S1 165 MET cc_start: 0.8600 (tmm) cc_final: 0.8236 (ttt) REVERT: S1 231 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7835 (mt-10) REVERT: S1 461 LYS cc_start: 0.9036 (tptm) cc_final: 0.8583 (tttm) REVERT: S1 556 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8302 (pp) REVERT: S1 604 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8602 (tm-30) REVERT: S2 78 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (mm110) REVERT: S2 87 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8513 (mt-10) REVERT: S2 143 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8577 (tm-30) REVERT: S2 166 ASP cc_start: 0.8674 (t70) cc_final: 0.8265 (t0) REVERT: S2 212 GLN cc_start: 0.8616 (tp40) cc_final: 0.8230 (tp40) REVERT: S2 248 ASP cc_start: 0.7902 (m-30) cc_final: 0.7534 (t0) REVERT: S3 1 MET cc_start: 0.7678 (tmm) cc_final: 0.7236 (tmm) REVERT: S3 84 SER cc_start: 0.9082 (m) cc_final: 0.8713 (t) REVERT: S3 91 SER cc_start: 0.9323 (t) cc_final: 0.8895 (p) REVERT: S3 167 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7070 (mt-10) REVERT: S4 112 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7974 (t-90) REVERT: S6 39 GLN cc_start: 0.8582 (tp40) cc_final: 0.8357 (tp40) REVERT: S8 49 ARG cc_start: 0.8718 (ttm170) cc_final: 0.7174 (tpt170) REVERT: S8 59 ASP cc_start: 0.8521 (p0) cc_final: 0.8170 (p0) REVERT: S8 195 TYR cc_start: 0.8403 (m-80) cc_final: 0.8149 (m-80) REVERT: S8 213 GLU cc_start: 0.8638 (tp30) cc_final: 0.8258 (tp30) REVERT: V1 268 THR cc_start: 0.8725 (p) cc_final: 0.8487 (p) REVERT: V1 297 ASN cc_start: 0.8523 (m110) cc_final: 0.8108 (t0) REVERT: V1 321 SER cc_start: 0.8684 (m) cc_final: 0.7722 (p) REVERT: V1 390 ASP cc_start: 0.7816 (m-30) cc_final: 0.7554 (m-30) REVERT: V1 435 GLU cc_start: 0.8671 (mp0) cc_final: 0.8179 (mp0) REVERT: 1M 57 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8493 (tttp) REVERT: 1M 102 ASP cc_start: 0.8290 (t0) cc_final: 0.7976 (t0) REVERT: 1M 198 THR cc_start: 0.9075 (p) cc_final: 0.8588 (p) REVERT: 2M 105 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8048 (tp30) REVERT: 2M 243 TYR cc_start: 0.7846 (m-80) cc_final: 0.7618 (m-10) REVERT: 2M 244 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8368 (tm-30) REVERT: 2M 434 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7091 (tmtt) REVERT: 2M 436 MET cc_start: 0.7984 (mmm) cc_final: 0.6414 (ppp) REVERT: 3M 96 MET cc_start: 0.8601 (mmp) cc_final: 0.8224 (mmt) REVERT: 3M 115 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (pp) REVERT: 4L 6 TYR cc_start: 0.8826 (m-80) cc_final: 0.8456 (m-80) REVERT: 4L 26 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7076 (mtt180) REVERT: 6M 32 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8960 (tt) REVERT: 6M 70 MET cc_start: 0.9043 (mmp) cc_final: 0.8616 (mmt) REVERT: A1 4 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8405 (tpp-160) REVERT: A1 6 MET cc_start: 0.8406 (mtp) cc_final: 0.8183 (ttm) REVERT: A1 49 MET cc_start: 0.8543 (mmp) cc_final: 0.8012 (mmm) REVERT: A1 52 ARG cc_start: 0.8517 (ttt-90) cc_final: 0.8222 (ttt90) REVERT: A8 19 MET cc_start: 0.8678 (mmm) cc_final: 0.8340 (mtp) REVERT: A8 45 ASN cc_start: 0.8684 (t0) cc_final: 0.8036 (t0) REVERT: A8 94 LYS cc_start: 0.8830 (tptp) cc_final: 0.8402 (mmtp) REVERT: AM 85 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8888 (tp) REVERT: C2 21 ASN cc_start: 0.8832 (m-40) cc_final: 0.8603 (m-40) REVERT: C2 26 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9116 (pp) REVERT: P2 105 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8133 (mmmm) REVERT: S5 11 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8391 (ttmm) REVERT: S5 27 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7734 (ttp80) REVERT: S5 38 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7739 (ttt180) REVERT: X1 10 LYS cc_start: 0.8563 (mttt) cc_final: 0.8209 (ttmm) REVERT: X1 29 PHE cc_start: 0.8958 (m-10) cc_final: 0.8546 (m-10) REVERT: X1 88 PHE cc_start: 0.9041 (m-80) cc_final: 0.8743 (m-80) REVERT: G1 80 TRP cc_start: 0.8999 (m100) cc_final: 0.8542 (m100) REVERT: G1 138 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8110 (p) REVERT: L2 103 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8330 (ttp80) REVERT: L2 165 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8145 (m170) REVERT: L2 181 GLU cc_start: 0.7936 (tt0) cc_final: 0.7646 (tt0) REVERT: L2 246 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7493 (tm-30) outliers start: 209 outliers final: 156 residues processed: 1376 average time/residue: 0.1697 time to fit residues: 391.0122 Evaluate side-chains 1378 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1210 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 216 MET Chi-restraints excluded: chain A9 residue 290 LEU Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 332 ILE Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 346 ILE Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 174 CYS Chi-restraints excluded: chain S1 residue 268 ILE Chi-restraints excluded: chain S1 residue 275 THR Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 292 GLU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 431 SER Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S2 residue 62 GLN Chi-restraints excluded: chain S2 residue 78 GLN Chi-restraints excluded: chain S2 residue 167 LEU Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 162 LYS Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 70 LEU Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 112 HIS Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 167 VAL Chi-restraints excluded: chain S7 residue 171 ASP Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 177 ILE Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 89 ASP Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 141 LEU Chi-restraints excluded: chain V1 residue 158 ILE Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 270 VAL Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain V2 residue 235 THR Chi-restraints excluded: chain 1M residue 57 LYS Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 119 TYR Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 248 LEU Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 266 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 435 ARG Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 64 SER Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 37 LEU Chi-restraints excluded: chain 4L residue 46 PHE Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 135 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A3 residue 33 VAL Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 38 ARG Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 32 ASN Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 73 VAL Chi-restraints excluded: chain G1 residue 138 THR Chi-restraints excluded: chain G1 residue 197 MET Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 94 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 168 LEU Chi-restraints excluded: chain G2 residue 169 VAL Chi-restraints excluded: chain G2 residue 173 THR Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 88 VAL Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 194 SER Chi-restraints excluded: chain L2 residue 238 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 514 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 357 optimal weight: 3.9990 chunk 541 optimal weight: 2.9990 chunk 473 optimal weight: 10.0000 chunk 531 optimal weight: 0.0040 chunk 438 optimal weight: 4.9990 chunk 493 optimal weight: 2.9990 chunk 415 optimal weight: 1.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A9 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 62 GLN ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 236 HIS ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 36 GLN G2 160 ASN G2 218 ASN L2 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.103908 restraints weight = 66264.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.106463 restraints weight = 43066.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.108005 restraints weight = 30914.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.109054 restraints weight = 23616.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109596 restraints weight = 20450.299| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.247 46100 Z= 0.359 Angle : 2.155 59.458 62544 Z= 1.252 Chirality : 0.372 6.354 6946 Planarity : 0.005 0.091 7932 Dihedral : 7.124 87.009 6481 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.79 % Favored : 89.14 % Rotamer: Outliers : 4.59 % Allowed : 25.63 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.12), residues: 5572 helix: 1.26 (0.10), residues: 2704 sheet: -1.41 (0.26), residues: 428 loop : -2.79 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGV1 330 TYR 0.060 0.002 TYR2M 149 PHE 0.040 0.002 PHEA9 371 TRP 0.032 0.002 TRPA5 109 HIS 0.008 0.001 HISG1 130 Details of bonding type rmsd covalent geometry : bond 0.01019 (46061) covalent geometry : angle 1.93834 (62467) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.93333 ( 14) hydrogen bonds : bond 0.05117 ( 2233) hydrogen bonds : angle 5.08140 ( 6492) metal coordination : bond 0.02055 ( 32) metal coordination : angle 29.75049 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 1238 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 38 GLU cc_start: 0.7222 (pt0) cc_final: 0.6959 (tt0) REVERT: A2 73 LYS cc_start: 0.8325 (mptt) cc_final: 0.8102 (mmtt) REVERT: A5 80 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8367 (ttm170) REVERT: A5 88 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A7 52 GLU cc_start: 0.7430 (mp0) cc_final: 0.7001 (mp0) REVERT: A7 92 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7904 (tm-30) REVERT: A7 109 TYR cc_start: 0.8838 (t80) cc_final: 0.7999 (t80) REVERT: A9 222 ARG cc_start: 0.8514 (mpp80) cc_final: 0.8078 (mtt180) REVERT: AL 45 ASN cc_start: 0.8515 (m-40) cc_final: 0.8288 (m-40) REVERT: AL 77 TYR cc_start: 0.8912 (m-80) cc_final: 0.8544 (m-80) REVERT: AL 134 SER cc_start: 0.9044 (p) cc_final: 0.8828 (t) REVERT: S1 58 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8068 (ttm110) REVERT: S1 117 ASN cc_start: 0.8319 (t0) cc_final: 0.7911 (t0) REVERT: S1 124 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: S1 165 MET cc_start: 0.8654 (tmm) cc_final: 0.8259 (ttt) REVERT: S1 231 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7845 (mt-10) REVERT: S1 461 LYS cc_start: 0.9055 (tptm) cc_final: 0.8617 (tttm) REVERT: S1 556 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8309 (pp) REVERT: S1 604 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8561 (tm-30) REVERT: S2 78 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8555 (mm110) REVERT: S2 87 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8571 (mt-10) REVERT: S2 166 ASP cc_start: 0.8685 (t70) cc_final: 0.8282 (t0) REVERT: S2 212 GLN cc_start: 0.8692 (tp40) cc_final: 0.8249 (tp40) REVERT: S3 1 MET cc_start: 0.7610 (tmm) cc_final: 0.7231 (tmm) REVERT: S3 84 SER cc_start: 0.9020 (m) cc_final: 0.8668 (t) REVERT: S3 91 SER cc_start: 0.9336 (t) cc_final: 0.8893 (p) REVERT: S4 112 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7825 (t-90) REVERT: S6 39 GLN cc_start: 0.8572 (tp40) cc_final: 0.8329 (tp40) REVERT: S8 49 ARG cc_start: 0.8707 (ttm170) cc_final: 0.7164 (tpt170) REVERT: S8 59 ASP cc_start: 0.8525 (p0) cc_final: 0.8170 (p0) REVERT: S8 195 TYR cc_start: 0.8563 (m-80) cc_final: 0.8294 (m-80) REVERT: S8 213 GLU cc_start: 0.8707 (tp30) cc_final: 0.8303 (tp30) REVERT: V1 132 LYS cc_start: 0.8506 (ptpt) cc_final: 0.7939 (tptm) REVERT: V1 144 ASN cc_start: 0.9251 (t0) cc_final: 0.8770 (t0) REVERT: V1 165 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8462 (mmtm) REVERT: V1 193 GLU cc_start: 0.8329 (mp0) cc_final: 0.8023 (mp0) REVERT: V1 268 THR cc_start: 0.8748 (p) cc_final: 0.8522 (p) REVERT: V1 297 ASN cc_start: 0.8562 (m110) cc_final: 0.8110 (t0) REVERT: V1 321 SER cc_start: 0.8817 (m) cc_final: 0.7833 (p) REVERT: V1 324 LEU cc_start: 0.8835 (mm) cc_final: 0.8604 (mm) REVERT: V1 390 ASP cc_start: 0.7858 (m-30) cc_final: 0.7575 (m-30) REVERT: V1 435 GLU cc_start: 0.8734 (mp0) cc_final: 0.8207 (mp0) REVERT: 1M 57 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8526 (tttp) REVERT: 1M 102 ASP cc_start: 0.8354 (t0) cc_final: 0.8032 (t0) REVERT: 1M 189 MET cc_start: 0.8201 (mtm) cc_final: 0.7931 (mtm) REVERT: 1M 198 THR cc_start: 0.9038 (p) cc_final: 0.8815 (p) REVERT: 2M 105 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8099 (tp30) REVERT: 2M 244 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8378 (tm-30) REVERT: 2M 434 LYS cc_start: 0.7483 (mmtm) cc_final: 0.7152 (tmtt) REVERT: 2M 436 MET cc_start: 0.7933 (mmm) cc_final: 0.6472 (tmm) REVERT: 3M 96 MET cc_start: 0.8657 (mmp) cc_final: 0.8284 (mmt) REVERT: 3M 115 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8966 (pp) REVERT: 4L 6 TYR cc_start: 0.8859 (m-80) cc_final: 0.8495 (m-80) REVERT: 4L 26 ARG cc_start: 0.7476 (mmm160) cc_final: 0.7042 (mtt180) REVERT: 6M 70 MET cc_start: 0.9064 (mmp) cc_final: 0.8633 (mmt) REVERT: A1 4 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8442 (tpp-160) REVERT: A1 6 MET cc_start: 0.8436 (mtp) cc_final: 0.8222 (ttm) REVERT: A1 49 MET cc_start: 0.8538 (mmp) cc_final: 0.8182 (mmm) REVERT: A1 52 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8306 (ttt90) REVERT: A8 19 MET cc_start: 0.8705 (mmm) cc_final: 0.8369 (mtp) REVERT: A8 45 ASN cc_start: 0.8730 (t0) cc_final: 0.8052 (t0) REVERT: AM 85 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8925 (tp) REVERT: C2 26 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9246 (pp) REVERT: P2 105 LYS cc_start: 0.8530 (mmtp) cc_final: 0.8137 (mmmm) REVERT: S5 11 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8286 (ttmm) REVERT: X1 10 LYS cc_start: 0.8573 (mttt) cc_final: 0.8180 (ttmm) REVERT: X1 29 PHE cc_start: 0.8986 (m-10) cc_final: 0.8577 (m-10) REVERT: G1 35 PHE cc_start: 0.9117 (p90) cc_final: 0.8778 (p90) REVERT: G1 80 TRP cc_start: 0.8976 (m100) cc_final: 0.8572 (m100) REVERT: G2 20 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8397 (mt0) REVERT: L2 71 LYS cc_start: 0.8972 (tmmt) cc_final: 0.8758 (ttmt) REVERT: L2 103 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8408 (ttp80) REVERT: L2 165 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8251 (m170) REVERT: L2 246 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 218 outliers final: 180 residues processed: 1364 average time/residue: 0.1580 time to fit residues: 362.3337 Evaluate side-chains 1386 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1197 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A5 residue 111 VAL Chi-restraints excluded: chain A7 residue 24 THR Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 50 VAL Chi-restraints excluded: chain A9 residue 64 ILE Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 216 MET Chi-restraints excluded: chain A9 residue 290 LEU Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 332 ILE Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 346 ILE Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 75 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 59 SER Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 174 CYS Chi-restraints excluded: chain S1 residue 215 VAL Chi-restraints excluded: chain S1 residue 268 ILE Chi-restraints excluded: chain S1 residue 275 THR Chi-restraints excluded: chain S1 residue 292 GLU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 431 SER Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 496 ILE Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 588 ASP Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S2 residue 78 GLN Chi-restraints excluded: chain S2 residue 167 LEU Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 368 PHE Chi-restraints excluded: chain S2 residue 387 ILE Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 121 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 162 LYS Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 112 HIS Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 167 VAL Chi-restraints excluded: chain S7 residue 171 ASP Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 177 ILE Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 89 ASP Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 141 LEU Chi-restraints excluded: chain V1 residue 158 ILE Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 222 ASP Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 282 ILE Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 33 ASP Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain V2 residue 235 THR Chi-restraints excluded: chain 1M residue 57 LYS Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 119 TYR Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 186 VAL Chi-restraints excluded: chain 1M residue 242 LEU Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 69 HIS Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 127 PHE Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 186 ILE Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 435 ARG Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 456 LEU Chi-restraints excluded: chain 2M residue 465 ILE Chi-restraints excluded: chain 3M residue 24 LEU Chi-restraints excluded: chain 3M residue 64 SER Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 115 LEU Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 46 PHE Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 4L residue 72 GLU Chi-restraints excluded: chain 6M residue 15 LEU Chi-restraints excluded: chain 6M residue 25 HIS Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 121 SER Chi-restraints excluded: chain 6M residue 135 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A1 residue 31 LYS Chi-restraints excluded: chain A3 residue 33 VAL Chi-restraints excluded: chain A8 residue 64 LEU Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 47 VAL Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 53 ILE Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 46 MET Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 73 VAL Chi-restraints excluded: chain G1 residue 128 VAL Chi-restraints excluded: chain G1 residue 153 ASP Chi-restraints excluded: chain G1 residue 197 MET Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 94 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 168 LEU Chi-restraints excluded: chain G2 residue 169 VAL Chi-restraints excluded: chain G2 residue 173 THR Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 88 VAL Chi-restraints excluded: chain L2 residue 105 ASP Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 194 SER Chi-restraints excluded: chain L2 residue 238 TYR Chi-restraints excluded: chain L2 residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 240 optimal weight: 0.9980 chunk 416 optimal weight: 0.7980 chunk 534 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 471 optimal weight: 5.9990 chunk 344 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A9 248 GLN ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 236 HIS 2M 332 GLN 2M 481 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 36 GLN G2 218 ASN L2 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.129376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.109541 restraints weight = 66404.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112171 restraints weight = 42680.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113738 restraints weight = 30281.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.115194 restraints weight = 23178.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.115381 restraints weight = 19347.436| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.247 46100 Z= 0.345 Angle : 2.146 58.795 62544 Z= 1.249 Chirality : 0.372 6.344 6946 Planarity : 0.005 0.087 7932 Dihedral : 6.975 89.297 6481 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.79 % Rotamer: Outliers : 3.79 % Allowed : 26.60 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 5572 helix: 1.34 (0.10), residues: 2695 sheet: -1.40 (0.27), residues: 410 loop : -2.71 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGV1 330 TYR 0.061 0.002 TYR2M 149 PHE 0.040 0.001 PHEA9 371 TRP 0.031 0.001 TRPA5 109 HIS 0.006 0.001 HISV1 450 Details of bonding type rmsd covalent geometry : bond 0.00992 (46061) covalent geometry : angle 1.93445 (62467) SS BOND : bond 0.00384 ( 7) SS BOND : angle 1.64509 ( 14) hydrogen bonds : bond 0.04682 ( 2233) hydrogen bonds : angle 4.98784 ( 6492) metal coordination : bond 0.01696 ( 32) metal coordination : angle 29.34991 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1247 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 73 LYS cc_start: 0.8307 (mptt) cc_final: 0.8104 (mmtt) REVERT: A5 88 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A7 52 GLU cc_start: 0.7431 (mp0) cc_final: 0.6991 (mp0) REVERT: A7 92 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7900 (tm-30) REVERT: A7 109 TYR cc_start: 0.8750 (t80) cc_final: 0.7896 (t80) REVERT: A9 290 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7043 (tt) REVERT: A9 306 PHE cc_start: 0.7595 (p90) cc_final: 0.6896 (m-80) REVERT: AL 45 ASN cc_start: 0.8470 (m-40) cc_final: 0.8259 (m-40) REVERT: AL 134 SER cc_start: 0.9000 (p) cc_final: 0.8775 (t) REVERT: S1 58 ARG cc_start: 0.8325 (tpp80) cc_final: 0.8041 (ttm110) REVERT: S1 117 ASN cc_start: 0.8234 (t0) cc_final: 0.7791 (t0) REVERT: S1 124 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: S1 165 MET cc_start: 0.8584 (tmm) cc_final: 0.8279 (ttp) REVERT: S1 461 LYS cc_start: 0.9024 (tptm) cc_final: 0.8754 (tttm) REVERT: S1 556 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8284 (pp) REVERT: S1 604 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8623 (tm-30) REVERT: S2 78 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8469 (mm110) REVERT: S2 87 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8508 (mt-10) REVERT: S2 166 ASP cc_start: 0.8678 (t70) cc_final: 0.8265 (t0) REVERT: S2 212 GLN cc_start: 0.8639 (tp40) cc_final: 0.8232 (tp40) REVERT: S2 303 LYS cc_start: 0.9091 (mttt) cc_final: 0.8792 (mttt) REVERT: S3 1 MET cc_start: 0.7613 (tmm) cc_final: 0.7232 (tmm) REVERT: S3 17 LYS cc_start: 0.9345 (ttpp) cc_final: 0.8790 (ttpt) REVERT: S3 84 SER cc_start: 0.9033 (m) cc_final: 0.8684 (t) REVERT: S3 91 SER cc_start: 0.9328 (t) cc_final: 0.8896 (p) REVERT: S3 167 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7063 (mt-10) REVERT: S4 112 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7648 (t-90) REVERT: S8 49 ARG cc_start: 0.8665 (ttm170) cc_final: 0.7122 (tpt170) REVERT: S8 59 ASP cc_start: 0.8506 (p0) cc_final: 0.8159 (p0) REVERT: S8 195 TYR cc_start: 0.8379 (m-80) cc_final: 0.8120 (m-80) REVERT: S8 213 GLU cc_start: 0.8591 (tp30) cc_final: 0.8192 (tp30) REVERT: V1 132 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7832 (tptm) REVERT: V1 147 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: V1 268 THR cc_start: 0.8753 (p) cc_final: 0.8531 (p) REVERT: V1 321 SER cc_start: 0.8707 (m) cc_final: 0.7740 (p) REVERT: V1 390 ASP cc_start: 0.7843 (m-30) cc_final: 0.7574 (m-30) REVERT: V1 435 GLU cc_start: 0.8635 (mp0) cc_final: 0.8142 (mp0) REVERT: 1M 57 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8507 (tttp) REVERT: 1M 189 MET cc_start: 0.8080 (mtm) cc_final: 0.7825 (mtm) REVERT: 1M 198 THR cc_start: 0.8933 (p) cc_final: 0.8730 (p) REVERT: 2M 105 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8103 (tp30) REVERT: 2M 145 SER cc_start: 0.8679 (t) cc_final: 0.8466 (t) REVERT: 2M 162 THR cc_start: 0.6065 (OUTLIER) cc_final: 0.5677 (m) REVERT: 2M 244 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8297 (tm-30) REVERT: 2M 265 ASN cc_start: 0.9288 (t0) cc_final: 0.9005 (t0) REVERT: 2M 385 PHE cc_start: 0.8825 (m-10) cc_final: 0.8614 (m-10) REVERT: 2M 434 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7062 (tmtt) REVERT: 2M 436 MET cc_start: 0.7935 (mmm) cc_final: 0.6353 (ppp) REVERT: 4L 6 TYR cc_start: 0.8844 (m-80) cc_final: 0.8438 (m-80) REVERT: 4L 26 ARG cc_start: 0.7372 (mmm160) cc_final: 0.6968 (mtt180) REVERT: 6M 32 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9041 (tt) REVERT: 6M 70 MET cc_start: 0.9029 (mmp) cc_final: 0.8522 (mmt) REVERT: A1 4 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8425 (tpp-160) REVERT: A1 6 MET cc_start: 0.8383 (mtp) cc_final: 0.8155 (ttm) REVERT: A1 49 MET cc_start: 0.8503 (mmp) cc_final: 0.8211 (mmm) REVERT: A1 52 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8136 (ttt90) REVERT: A1 54 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8791 (tttm) REVERT: A8 19 MET cc_start: 0.8632 (mmm) cc_final: 0.8404 (mtp) REVERT: A8 42 LYS cc_start: 0.8594 (tptp) cc_final: 0.7960 (mttm) REVERT: A8 45 ASN cc_start: 0.8698 (t0) cc_final: 0.8047 (t0) REVERT: A8 78 TYR cc_start: 0.8981 (t80) cc_final: 0.8659 (t80) REVERT: A8 94 LYS cc_start: 0.8792 (tptp) cc_final: 0.8414 (mmtp) REVERT: AM 85 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (tp) REVERT: C2 26 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9167 (pp) REVERT: S5 27 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7715 (ttp80) REVERT: X1 10 LYS cc_start: 0.8611 (mttt) cc_final: 0.8192 (ttmm) REVERT: X1 29 PHE cc_start: 0.8917 (m-10) cc_final: 0.8542 (m-10) REVERT: G1 35 PHE cc_start: 0.8954 (p90) cc_final: 0.8560 (p90) REVERT: G2 17 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7719 (mm-30) REVERT: G2 147 MET cc_start: 0.7277 (mmt) cc_final: 0.6911 (mmt) REVERT: L2 103 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8303 (ttp80) REVERT: L2 165 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8150 (m170) outliers start: 180 outliers final: 147 residues processed: 1355 average time/residue: 0.1574 time to fit residues: 356.5554 Evaluate side-chains 1374 residues out of total 4779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1215 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 97 LEU Chi-restraints excluded: chain A5 residue 111 VAL Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 50 VAL Chi-restraints excluded: chain A9 residue 64 ILE Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 105 LEU Chi-restraints excluded: chain A9 residue 290 LEU Chi-restraints excluded: chain A9 residue 302 VAL Chi-restraints excluded: chain A9 residue 332 ILE Chi-restraints excluded: chain A9 residue 342 THR Chi-restraints excluded: chain A9 residue 346 ILE Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 357 LEU Chi-restraints excluded: chain A9 residue 360 ILE Chi-restraints excluded: chain A9 residue 362 HIS Chi-restraints excluded: chain AL residue 44 HIS Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 103 THR Chi-restraints excluded: chain S1 residue 79 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 124 GLU Chi-restraints excluded: chain S1 residue 128 SER Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 174 CYS Chi-restraints excluded: chain S1 residue 215 VAL Chi-restraints excluded: chain S1 residue 268 ILE Chi-restraints excluded: chain S1 residue 275 THR Chi-restraints excluded: chain S1 residue 288 LEU Chi-restraints excluded: chain S1 residue 292 GLU Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 360 VAL Chi-restraints excluded: chain S1 residue 374 HIS Chi-restraints excluded: chain S1 residue 431 SER Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 507 LEU Chi-restraints excluded: chain S1 residue 556 LEU Chi-restraints excluded: chain S1 residue 630 THR Chi-restraints excluded: chain S1 residue 673 THR Chi-restraints excluded: chain S2 residue 78 GLN Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 253 THR Chi-restraints excluded: chain S2 residue 368 PHE Chi-restraints excluded: chain S2 residue 392 VAL Chi-restraints excluded: chain S3 residue 86 ILE Chi-restraints excluded: chain S3 residue 89 GLN Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 115 VAL Chi-restraints excluded: chain S3 residue 143 LEU Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 67 ILE Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 112 HIS Chi-restraints excluded: chain S7 residue 70 LEU Chi-restraints excluded: chain S7 residue 126 LEU Chi-restraints excluded: chain S7 residue 167 VAL Chi-restraints excluded: chain S7 residue 171 ASP Chi-restraints excluded: chain S7 residue 180 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 129 CYS Chi-restraints excluded: chain S8 residue 172 CYS Chi-restraints excluded: chain S8 residue 177 ILE Chi-restraints excluded: chain S8 residue 209 THR Chi-restraints excluded: chain V1 residue 63 LEU Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 101 THR Chi-restraints excluded: chain V1 residue 141 LEU Chi-restraints excluded: chain V1 residue 147 GLU Chi-restraints excluded: chain V1 residue 158 ILE Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 222 ASP Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 282 ILE Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V1 residue 474 LEU Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 179 VAL Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain V2 residue 219 THR Chi-restraints excluded: chain V2 residue 235 THR Chi-restraints excluded: chain 1M residue 43 VAL Chi-restraints excluded: chain 1M residue 57 LYS Chi-restraints excluded: chain 1M residue 99 VAL Chi-restraints excluded: chain 1M residue 119 TYR Chi-restraints excluded: chain 1M residue 153 LEU Chi-restraints excluded: chain 1M residue 161 CYS Chi-restraints excluded: chain 2M residue 65 LEU Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 110 ASP Chi-restraints excluded: chain 2M residue 127 PHE Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 255 SER Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 390 ILE Chi-restraints excluded: chain 2M residue 423 VAL Chi-restraints excluded: chain 2M residue 435 ARG Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 456 LEU Chi-restraints excluded: chain 2M residue 465 ILE Chi-restraints excluded: chain 3M residue 64 SER Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 83 SER Chi-restraints excluded: chain 3M residue 116 ASP Chi-restraints excluded: chain 4L residue 46 PHE Chi-restraints excluded: chain 4L residue 53 LEU Chi-restraints excluded: chain 6M residue 32 LEU Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 117 ILE Chi-restraints excluded: chain 6M residue 135 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A3 residue 33 VAL Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 20 VAL Chi-restraints excluded: chain AM residue 47 VAL Chi-restraints excluded: chain AM residue 85 ILE Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain S5 residue 52 GLN Chi-restraints excluded: chain X1 residue 16 VAL Chi-restraints excluded: chain X1 residue 26 VAL Chi-restraints excluded: chain X1 residue 68 ILE Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 46 MET Chi-restraints excluded: chain G1 residue 67 LEU Chi-restraints excluded: chain G1 residue 153 ASP Chi-restraints excluded: chain G1 residue 197 MET Chi-restraints excluded: chain G1 residue 210 LEU Chi-restraints excluded: chain G2 residue 59 VAL Chi-restraints excluded: chain G2 residue 71 VAL Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 168 LEU Chi-restraints excluded: chain G2 residue 169 VAL Chi-restraints excluded: chain L2 residue 56 TYR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 88 VAL Chi-restraints excluded: chain L2 residue 145 ILE Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 194 SER Chi-restraints excluded: chain L2 residue 238 TYR Chi-restraints excluded: chain L2 residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 475 optimal weight: 2.9990 chunk 484 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 456 optimal weight: 0.5980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A9 248 GLN ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 236 HIS ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 218 ASN L2 81 ASN ** L2 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.107005 restraints weight = 66768.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109610 restraints weight = 43433.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111333 restraints weight = 30931.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.112355 restraints weight = 23191.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112796 restraints weight = 20339.924| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.246 46100 Z= 0.350 Angle : 2.151 59.668 62544 Z= 1.250 Chirality : 0.372 6.347 6946 Planarity : 0.005 0.090 7932 Dihedral : 6.963 89.569 6481 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.28 % Favored : 89.68 % Rotamer: Outliers : 3.87 % Allowed : 26.89 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 5572 helix: 1.37 (0.10), residues: 2696 sheet: -1.41 (0.27), residues: 410 loop : -2.70 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGV1 330 TYR 0.060 0.002 TYR2M 149 PHE 0.040 0.002 PHEA9 371 TRP 0.035 0.001 TRP1M 251 HIS 0.006 0.001 HISV1 450 Details of bonding type rmsd covalent geometry : bond 0.01002 (46061) covalent geometry : angle 1.93758 (62467) SS BOND : bond 0.00473 ( 7) SS BOND : angle 1.79754 ( 14) hydrogen bonds : bond 0.04832 ( 2233) hydrogen bonds : angle 4.99563 ( 6492) metal coordination : bond 0.01782 ( 32) metal coordination : angle 29.47979 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8924.27 seconds wall clock time: 153 minutes 31.34 seconds (9211.34 seconds total)