Starting phenix.real_space_refine on Tue Aug 26 23:52:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.map" model { file = "/net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oa1_3727/08_2025/5oa1_3727.cif" } resolution = 4.4 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 105 5.49 5 S 193 5.16 5 C 26700 2.51 5 N 7806 2.21 5 O 8648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43459 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 11513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11513 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 9 Chain: "B" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9327 Classifications: {'peptide': 1175} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1115} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1028 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "T" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1128 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "U" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 1164 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 283} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 8 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1307 Unresolved non-hydrogen angles: 1874 Unresolved non-hydrogen dihedrals: 871 Unresolved non-hydrogen chiralities: 379 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 9, 'ARG:plan': 18, 'TRP:plan': 6, 'GLN:plan1': 16, 'TYR:plan': 12, 'HIS:plan': 9, 'GLU:plan': 16, 'PHE:plan': 12} Unresolved non-hydrogen planarities: 588 Chain: "V" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 1152 Classifications: {'peptide': 288} Incomplete info: {'backbone_only': 274} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1234 Unresolved non-hydrogen angles: 1792 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 371 Planarities with less than four sites: {'ASP:plan': 20, 'GLN:plan1': 12, 'ASN:plan1': 17, 'ARG:plan': 17, 'TYR:plan': 9, 'GLU:plan': 14, 'HIS:plan': 9, 'PHE:plan': 14, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 611 Chain: "W" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 672 Classifications: {'peptide': 168} Incomplete info: {'backbone_only': 165} Link IDs: {'TRANS': 167} Chain breaks: 7 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 1108 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 11, 'TYR:plan': 6, 'HIS:plan': 7, 'ASP:plan': 9, 'TRP:plan': 6, 'PHE:plan': 7, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 384 Chain: "1" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 52 Classifications: {'peptide': 13} Incomplete info: {'backbone_only': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 76 Classifications: {'peptide': 19} Incomplete info: {'backbone_only': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen chiralities: 19 Chain: "3" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 36 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "4" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 92 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen chiralities: 23 Chain: "5" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 64 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Classifications: {'peptide': 10} Incomplete info: {'backbone_only': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "7" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 100 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen chiralities: 25 Chain: "8" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Classifications: {'peptide': 10} Incomplete info: {'backbone_only': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "9" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 36 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 64 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 16} Link IDs: {'TRANS': 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "P" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen chiralities: 22 Chain: "Z" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 60 Classifications: {'peptide': 15} Incomplete info: {'backbone_only': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "Y" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 48 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 108 Classifications: {'peptide': 27} Incomplete info: {'backbone_only': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen chiralities: 27 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 133.009 51.455 76.703 1.00108.95 S ATOM 806 SG CYS A 105 131.957 48.185 75.238 1.00111.29 S ATOM 1605 SG CYS A 233 132.833 48.299 78.974 1.00112.17 S ATOM 1627 SG CYS A 236 135.518 48.791 75.920 1.00124.79 S ATOM 461 SG CYS A 62 89.436 71.280 58.000 1.00 94.92 S ATOM 480 SG CYS A 65 86.647 68.841 58.490 1.00 92.34 S ATOM 535 SG CYS A 72 87.444 70.978 61.201 1.00 92.92 S ATOM 20128 SG CYS B1104 92.582 53.653 62.185 1.00 81.64 S ATOM 20154 SG CYS B1107 95.298 55.126 63.877 1.00 88.74 S ATOM 20301 SG CYS B1128 93.955 56.840 60.906 1.00 84.61 S ATOM 20329 SG CYS B1131 95.842 53.421 60.578 1.00 88.47 S ATOM 29064 SG CYS I 13 143.994 103.105 130.171 1.00161.37 S ATOM 29184 SG CYS I 30 146.200 100.497 128.678 1.00194.69 S ATOM 29975 SG CYS J 7 48.793 97.109 115.131 1.00101.98 S ATOM 29998 SG CYS J 10 44.893 95.822 115.263 1.00 97.69 S ATOM 30278 SG CYS J 45 47.767 95.180 118.171 1.00101.16 S ATOM 30284 SG CYS J 46 45.993 98.307 117.324 1.00101.59 S ATOM 31350 SG CYS L 31 73.249 123.402 89.026 1.00125.00 S ATOM 31370 SG CYS L 34 71.757 126.608 89.663 1.00127.07 S ATOM 31474 SG CYS L 48 72.648 125.910 86.175 1.00139.22 S ATOM 31497 SG CYS L 51 75.342 126.655 89.646 1.00135.61 S Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" P DG S 7 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 7 " occ=0.00 residue: pdb=" P DT S 8 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 8 " occ=0.00 residue: pdb=" P DC S 9 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC S 9 " occ=0.00 residue: pdb=" P DA S 10 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 10 " occ=0.00 residue: pdb=" P DT S 11 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 11 " occ=0.00 residue: pdb=" P DG S 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 12 " occ=0.00 residue: pdb=" P DG S 13 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 13 " occ=0.00 residue: pdb=" P DA S 14 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 14 " occ=0.00 residue: pdb=" P DG S 15 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 15 " occ=0.00 residue: pdb=" P DT S 16 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 16 " occ=0.00 residue: pdb=" P DA S 17 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 17 " occ=0.00 residue: pdb=" P DC S 18 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC S 18 " occ=0.00 ... (remaining 48 not shown) Time building chain proxies: 8.62, per 1000 atoms: 0.20 Number of scatterers: 43459 At special positions: 0 Unit cell: (167.4, 210.6, 179.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 193 16.00 P 105 15.00 O 8648 8.00 N 7806 7.00 C 26700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 27 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8858 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 58 sheets defined 44.7% alpha, 17.4% beta 33 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.707A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.645A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.664A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.875A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.917A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.665A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.101A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 400 removed outlier: 4.161A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.549A pdb=" N LYS A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.737A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.521A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.508A pdb=" N THR A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.614A pdb=" N SER A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.589A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.780A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.666A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.550A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.586A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.579A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 3.677A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.563A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.659A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 removed outlier: 3.607A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.586A pdb=" N VAL A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1266' Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.525A pdb=" N VAL A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1338 Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.719A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.609A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.988A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.677A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.010A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.631A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.664A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 4.142A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.718A pdb=" N LEU B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.553A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.528A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.794A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.094A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.842A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.696A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.005A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.531A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.523A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.570A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.541A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.804A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1136 through 1138 No H-bonds generated for 'chain 'B' and resid 1136 through 1138' Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.643A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.561A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.903A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.500A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.972A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.541A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.655A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.590A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.646A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.623A pdb=" N SER E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.518A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.558A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.666A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 removed outlier: 3.943A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.939A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 132' Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.954A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.050A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.977A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'O' and resid 49 through 65 removed outlier: 3.531A pdb=" N SER O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 removed outlier: 3.637A pdb=" N LEU O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 removed outlier: 3.788A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 107 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 124 through 128 Processing helix chain 'O' and resid 129 through 147 removed outlier: 3.727A pdb=" N SER O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.579A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 164 No H-bonds generated for 'chain 'O' and resid 162 through 164' Processing helix chain 'O' and resid 169 through 183 Processing helix chain 'O' and resid 186 through 197 Processing helix chain 'O' and resid 204 through 220 removed outlier: 3.685A pdb=" N LEU O 215 " --> pdb=" O TYR O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 247 Processing helix chain 'O' and resid 325 through 347 removed outlier: 3.554A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 354 Processing helix chain 'O' and resid 356 through 373 Processing helix chain 'O' and resid 381 through 390 removed outlier: 4.222A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN O 390 " --> pdb=" O PHE O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 408 removed outlier: 3.828A pdb=" N PHE O 408 " --> pdb=" O ILE O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 431 removed outlier: 3.668A pdb=" N ILE O 418 " --> pdb=" O ALA O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 456 removed outlier: 3.625A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 Processing helix chain 'O' and resid 470 through 488 Processing helix chain 'O' and resid 489 through 491 No H-bonds generated for 'chain 'O' and resid 489 through 491' Processing helix chain 'O' and resid 498 through 500 No H-bonds generated for 'chain 'O' and resid 498 through 500' Processing helix chain 'O' and resid 501 through 511 removed outlier: 3.877A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET O 509 " --> pdb=" O PHE O 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.862A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 535 Processing helix chain 'O' and resid 540 through 551 Processing helix chain 'O' and resid 582 through 589 Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 608 through 610 No H-bonds generated for 'chain 'O' and resid 608 through 610' Processing helix chain 'U' and resid 97 through 124 removed outlier: 3.526A pdb=" N GLN U 115 " --> pdb=" O ILE U 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 124 " --> pdb=" O ILE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 147 removed outlier: 3.576A pdb=" N HIS U 131 " --> pdb=" O LYS U 127 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 138 " --> pdb=" O LYS U 134 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS U 142 " --> pdb=" O LEU U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 173 removed outlier: 3.596A pdb=" N THR U 161 " --> pdb=" O HIS U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 187 removed outlier: 3.503A pdb=" N LYS U 183 " --> pdb=" O CYS U 179 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP U 184 " --> pdb=" O ASP U 180 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 207 removed outlier: 3.747A pdb=" N GLN U 206 " --> pdb=" O SER U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 217 Processing helix chain 'U' and resid 227 through 237 removed outlier: 4.654A pdb=" N ALA U 231 " --> pdb=" O TYR U 227 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS U 234 " --> pdb=" O ILE U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 261 removed outlier: 4.270A pdb=" N LEU U 254 " --> pdb=" O GLN U 250 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS U 255 " --> pdb=" O GLY U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 281 Processing helix chain 'U' and resid 301 through 316 Processing helix chain 'U' and resid 405 through 417 removed outlier: 4.019A pdb=" N ALA U 409 " --> pdb=" O ASP U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 448 removed outlier: 3.545A pdb=" N GLU U 440 " --> pdb=" O LEU U 436 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 492 Processing helix chain 'U' and resid 495 through 514 removed outlier: 3.673A pdb=" N ASP U 500 " --> pdb=" O GLU U 496 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS U 501 " --> pdb=" O GLN U 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 226 removed outlier: 3.927A pdb=" N ARG W 211 " --> pdb=" O ASN W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 241 removed outlier: 4.288A pdb=" N ARG W 241 " --> pdb=" O ALA W 237 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 261 Processing helix chain 'W' and resid 269 through 278 removed outlier: 3.758A pdb=" N TRP W 273 " --> pdb=" O ASP W 269 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 321 removed outlier: 3.975A pdb=" N TYR W 312 " --> pdb=" O PHE W 308 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP W 314 " --> pdb=" O ILE W 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU W 317 " --> pdb=" O LEU W 313 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 353 removed outlier: 4.061A pdb=" N LEU W 342 " --> pdb=" O GLU W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 364 through 385 removed outlier: 3.665A pdb=" N LYS W 375 " --> pdb=" O CYS W 371 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 420 removed outlier: 3.526A pdb=" N ILE W 417 " --> pdb=" O THR W 413 " (cutoff:3.500A) Processing helix chain 'W' and resid 430 through 442 Processing helix chain '1' and resid 10 through 21 Processing helix chain '2' and resid 3 through 20 Processing helix chain '3' and resid 16 through 23 Processing helix chain '4' and resid 3 through 24 Processing helix chain '5' and resid 28 through 42 Processing helix chain '6' and resid 44 through 52 Processing helix chain '7' and resid 54 through 77 Processing helix chain '8' and resid 79 through 87 Processing helix chain '9' and resid 89 through 96 Processing helix chain 'Q' and resid 98 through 103 Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'P' and resid 115 through 135 Processing helix chain 'Z' and resid 137 through 150 Processing helix chain 'Y' and resid 152 through 162 Processing helix chain 'R' and resid 164 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.826A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 14 " --> pdb=" O ARG B1197 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG B1197 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 16 " --> pdb=" O ARG B1195 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B1195 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 6.319A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.781A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.863A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.708A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 removed outlier: 3.657A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.562A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.562A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB4, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.799A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 4.169A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1459 through 1462 removed outlier: 3.675A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.900A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.066A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.207A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 145 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.207A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.444A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.775A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC7, first strand: chain 'B' and resid 571 through 572 removed outlier: 7.044A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 740 through 744 removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 740 through 744 removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD2, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.556A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.541A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.359A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE L 67 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.768A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.365A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.520A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 132 through 140 removed outlier: 5.917A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS G 158 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.521A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AF2, first strand: chain 'I' and resid 98 through 99 removed outlier: 3.990A pdb=" N LEU I 99 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR I 109 " --> pdb=" O LEU I 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.766A pdb=" N ILE M 88 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.986A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 21 through 23 Processing sheet with id=AF7, first strand: chain 'V' and resid 10 through 17 removed outlier: 4.025A pdb=" N ASP V 10 " --> pdb=" O SER V 553 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR V 549 " --> pdb=" O SER V 14 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU V 16 " --> pdb=" O VAL V 547 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL V 547 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR V 513 " --> pdb=" O LEU V 541 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 181 through 184 removed outlier: 3.530A pdb=" N ARG V 181 " --> pdb=" O TYR V 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR V 234 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 244 through 246 removed outlier: 5.954A pdb=" N ARG V 273 " --> pdb=" O PRO V 291 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 302 through 307 removed outlier: 3.723A pdb=" N ASP V 304 " --> pdb=" O ILE V 318 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TRP V 324 " --> pdb=" O THR V 350 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR V 350 " --> pdb=" O TRP V 324 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE V 326 " --> pdb=" O HIS V 348 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 360 through 365 removed outlier: 3.517A pdb=" N LYS V 379 " --> pdb=" O ASP V 376 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP V 384 " --> pdb=" O TRP V 389 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP V 389 " --> pdb=" O ASP V 384 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 404 through 407 Processing sheet with id=AG4, first strand: chain 'V' and resid 448 through 453 removed outlier: 3.548A pdb=" N ARG V 450 " --> pdb=" O SER V 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY V 503 " --> pdb=" O MET V 478 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL V 480 " --> pdb=" O PRO V 501 " (cutoff:3.500A) 2093 hydrogen bonds defined for protein. 5907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 11.92 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.54: 40257 1.54 - 1.88: 4143 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.89: 12 Bond restraints: 44412 Sorted by residual: bond pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 1.332 2.834 -1.502 1.02e-02 9.61e+03 2.17e+04 bond pdb=" C PRO V 309 " pdb=" N ASP V 311 " ideal model delta sigma weight residual 1.331 2.803 -1.471 1.14e-02 7.69e+03 1.67e+04 bond pdb=" C PRO V 330 " pdb=" N ILE V 344 " ideal model delta sigma weight residual 1.335 2.772 -1.437 1.20e-02 6.94e+03 1.43e+04 bond pdb=" C SER V 427 " pdb=" N PRO V 432 " ideal model delta sigma weight residual 1.328 2.774 -1.446 1.25e-02 6.40e+03 1.34e+04 bond pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 1.332 2.886 -1.554 1.36e-02 5.41e+03 1.31e+04 ... (remaining 44407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.67: 59955 11.67 - 23.35: 33 23.35 - 35.02: 4 35.02 - 46.69: 9 46.69 - 58.37: 1 Bond angle restraints: 60002 Sorted by residual: angle pdb=" O SER V 207 " pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 123.27 64.90 58.37 1.16e+00 7.43e-01 2.53e+03 angle pdb=" O GLU V 355 " pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 122.08 78.20 43.88 1.07e+00 8.73e-01 1.68e+03 angle pdb=" CA SER V 207 " pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 116.39 72.13 44.26 1.17e+00 7.31e-01 1.43e+03 angle pdb=" O HIS V 483 " pdb=" C HIS V 483 " pdb=" N GLU V 499 " ideal model delta sigma weight residual 122.41 78.11 44.30 1.38e+00 5.25e-01 1.03e+03 angle pdb=" CA GLU V 355 " pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 116.79 81.83 34.96 1.28e+00 6.10e-01 7.46e+02 ... (remaining 59997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.43: 21579 18.43 - 36.86: 2332 36.86 - 55.29: 1042 55.29 - 73.72: 282 73.72 - 92.15: 101 Dihedral angle restraints: 25336 sinusoidal: 10708 harmonic: 14628 Sorted by residual: dihedral pdb=" CA LYS U 127 " pdb=" C LYS U 127 " pdb=" N GLU U 128 " pdb=" CA GLU U 128 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU O 434 " pdb=" C LEU O 434 " pdb=" N SER O 435 " pdb=" CA SER O 435 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA SER O 448 " pdb=" C SER O 448 " pdb=" N TRP O 449 " pdb=" CA TRP O 449 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 25333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 6056 0.186 - 0.372: 99 0.372 - 0.557: 15 0.557 - 0.743: 3 0.743 - 0.929: 1 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C1' DT T 42 " pdb=" O4' DT T 42 " pdb=" C2' DT T 42 " pdb=" N1 DT T 42 " both_signs ideal model delta sigma weight residual False 2.47 1.54 0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CG LEU O 180 " pdb=" CB LEU O 180 " pdb=" CD1 LEU O 180 " pdb=" CD2 LEU O 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C3' DC T 43 " pdb=" C4' DC T 43 " pdb=" O3' DC T 43 " pdb=" C2' DC T 43 " both_signs ideal model delta sigma weight residual False -2.66 -3.24 0.58 2.00e-01 2.50e+01 8.39e+00 ... (remaining 6171 not shown) Planarity restraints: 7686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS V 483 " -0.186 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C HIS V 483 " 0.446 2.00e-02 2.50e+03 pdb=" O HIS V 483 " -0.247 2.00e-02 2.50e+03 pdb=" N GLU V 499 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU V 355 " -0.190 2.00e-02 2.50e+03 2.63e-01 6.94e+02 pdb=" C GLU V 355 " 0.421 2.00e-02 2.50e+03 pdb=" O GLU V 355 " -0.253 2.00e-02 2.50e+03 pdb=" N SER V 358 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 442 " 0.155 2.00e-02 2.50e+03 2.38e-01 5.65e+02 pdb=" C LEU V 442 " -0.398 2.00e-02 2.50e+03 pdb=" O LEU V 442 " 0.205 2.00e-02 2.50e+03 pdb=" N ASP V 446 " 0.038 2.00e-02 2.50e+03 ... (remaining 7683 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.36: 31 1.36 - 2.24: 273 2.24 - 3.13: 30281 3.13 - 4.01: 116009 4.01 - 4.90: 201839 Warning: very small nonbonded interaction distances. Nonbonded interactions: 348433 Sorted by model distance: nonbonded pdb=" CD2 LEU B 898 " pdb=" CG2 VAL L 46 " model vdw 0.473 3.880 nonbonded pdb=" CG1 ILE G 139 " pdb=" OH TYR O 178 " model vdw 0.707 3.440 nonbonded pdb=" CD2 LEU B 95 " pdb=" CE1 PHE B 440 " model vdw 0.711 3.760 nonbonded pdb=" CG LEU B 95 " pdb=" CE2 PHE B 440 " model vdw 0.726 3.770 nonbonded pdb=" CD2 LEU B 95 " pdb=" CZ PHE B 440 " model vdw 0.827 3.760 ... (remaining 348428 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 Found NCS groups: ncs_group { reference = (chain '1' and resid 10 through 21) selection = chain 'Y' selection = (chain 'Z' and resid 139 through 150) } ncs_group { reference = chain '2' selection = (chain 'P' and resid 117 through 135) } ncs_group { reference = chain '3' selection = (chain '6' and resid 44 through 52) selection = (chain '8' and resid 79 through 87) selection = chain '9' } ncs_group { reference = chain '4' selection = (chain '7' and resid 55 through 77) selection = (chain 'R' and resid 167 through 189) } ncs_group { reference = chain '5' selection = chain 'Q' } 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=0.00 max=1.00 mean=0.97 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: 2.090 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 46.850 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.130 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 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 : 0.027 1.554 44443 Z= 2.091 Angle : 1.767 58.365 60029 Z= 1.225 Chirality : 0.074 0.929 6174 Planarity : 0.009 0.272 7686 Dihedral : 19.192 92.151 16478 Min Nonbonded Distance : 0.473 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 1.18 % Allowed : 5.42 % Favored : 93.40 % Rotamer: Outliers : 8.67 % Allowed : 10.59 % Favored : 80.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -1.92 (0.10), residues: 5498 helix: -0.78 (0.10), residues: 2196 sheet: -1.14 (0.17), residues: 729 loop : -1.69 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1091 TYR 0.043 0.006 TYR A1174 PHE 0.037 0.004 PHE B1044 TRP 0.039 0.005 TRP B 832 HIS 0.016 0.003 HIS B 646 Details of bonding type rmsd covalent geometry : bond 0.02666 (44412) covalent geometry : angle 1.75697 (60002) hydrogen bonds : bond 0.22747 ( 2132) hydrogen bonds : angle 8.36602 ( 6059) metal coordination : bond 0.10935 ( 22) metal coordination : angle 8.94719 ( 27) Misc. bond : bond 0.40584 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1900 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 362 poor density : 1538 time to evaluate : 1.127 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: symmetry 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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: 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: 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: 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: 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: 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: A 390 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5869 (mt) REVERT: A 485 SER cc_start: 0.9266 (m) cc_final: 0.8645 (p) REVERT: A 490 ILE cc_start: 0.9324 (pt) cc_final: 0.8801 (tt) REVERT: A 594 THR cc_start: 0.8338 (m) cc_final: 0.8010 (p) REVERT: A 597 LYS cc_start: 0.8943 (pttm) cc_final: 0.8712 (pttt) REVERT: A 600 MET cc_start: 0.7450 (ttt) cc_final: 0.6244 (ttt) REVERT: A 673 HIS cc_start: 0.7130 (m170) cc_final: 0.6596 (m170) REVERT: A 675 SER cc_start: 0.9452 (m) cc_final: 0.8976 (p) REVERT: A 690 GLU cc_start: 0.8126 (mp0) cc_final: 0.7843 (mp0) REVERT: A 822 THR cc_start: 0.9258 (m) cc_final: 0.8890 (p) REVERT: A 832 ASP cc_start: 0.8178 (m-30) cc_final: 0.7818 (m-30) REVERT: A 956 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7780 (mtt180) REVERT: A 977 MET cc_start: 0.7667 (ttt) cc_final: 0.6832 (ttt) REVERT: A 1032 VAL cc_start: 0.9169 (t) cc_final: 0.8890 (t) REVERT: A 1057 ILE cc_start: 0.8892 (mp) cc_final: 0.8668 (mt) REVERT: A 1080 TYR cc_start: 0.6800 (m-80) cc_final: 0.5931 (m-10) REVERT: A 1144 LEU cc_start: 0.9236 (tp) cc_final: 0.9025 (pp) REVERT: A 1190 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9023 (t) REVERT: A 1192 SER cc_start: 0.9219 (m) cc_final: 0.8859 (p) REVERT: A 1238 MET cc_start: 0.8106 (mtm) cc_final: 0.7589 (mtt) REVERT: A 1242 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 1434 GLU cc_start: 0.3664 (OUTLIER) cc_final: 0.2092 (pt0) REVERT: A 1530 TRP cc_start: 0.8727 (m-10) cc_final: 0.8506 (m-10) REVERT: A 1588 MET cc_start: 0.8229 (tpt) cc_final: 0.7861 (tpt) REVERT: A 1594 THR cc_start: 0.7437 (p) cc_final: 0.6834 (p) REVERT: B 21 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7773 (tpt170) REVERT: B 25 PHE cc_start: 0.8846 (m-10) cc_final: 0.8310 (m-10) REVERT: B 152 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 234 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 250 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 404 LEU cc_start: 0.9300 (mt) cc_final: 0.9080 (mt) REVERT: B 441 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5844 (mtpt) REVERT: B 465 LEU cc_start: 0.9105 (mt) cc_final: 0.8820 (mt) REVERT: B 480 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: B 491 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8383 (pp) REVERT: B 495 ARG cc_start: 0.9194 (tpt90) cc_final: 0.8823 (tpp80) REVERT: B 528 LEU cc_start: 0.9439 (mt) cc_final: 0.9229 (mt) REVERT: B 539 CYS cc_start: 0.7316 (t) cc_final: 0.6831 (t) REVERT: B 541 LEU cc_start: 0.8703 (mt) cc_final: 0.8366 (pp) REVERT: B 585 CYS cc_start: 0.6848 (t) cc_final: 0.5554 (t) REVERT: B 593 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.7619 (pp) REVERT: B 677 THR cc_start: 0.8107 (p) cc_final: 0.7557 (t) REVERT: B 699 ILE cc_start: 0.9275 (mt) cc_final: 0.8493 (mt) REVERT: B 719 CYS cc_start: 0.8812 (m) cc_final: 0.7953 (p) REVERT: B 803 MET cc_start: 0.8425 (ttp) cc_final: 0.8036 (tmm) REVERT: B 871 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6571 (pt) REVERT: B 907 ILE cc_start: 0.9195 (mp) cc_final: 0.8662 (mp) REVERT: B 915 ASP cc_start: 0.7069 (m-30) cc_final: 0.6786 (m-30) REVERT: B 937 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: B 962 MET cc_start: 0.8810 (ttt) cc_final: 0.8422 (tpp) REVERT: B 970 LYS cc_start: 0.9053 (ttpt) cc_final: 0.8744 (tppp) REVERT: B 985 ILE cc_start: 0.9358 (mm) cc_final: 0.9057 (mm) REVERT: B 1000 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 1033 TYR cc_start: 0.8309 (m-80) cc_final: 0.8024 (t80) REVERT: B 1092 LEU cc_start: 0.8033 (mt) cc_final: 0.7711 (mt) REVERT: B 1093 LEU cc_start: 0.7111 (tp) cc_final: 0.6598 (tp) REVERT: B 1120 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.3615 (pp) REVERT: C 191 ILE cc_start: 0.9444 (mt) cc_final: 0.9046 (tp) REVERT: C 196 LEU cc_start: 0.9368 (mp) cc_final: 0.8981 (mm) REVERT: C 259 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7907 (t70) REVERT: C 321 LEU cc_start: 0.8641 (tp) cc_final: 0.8437 (tp) REVERT: E 18 THR cc_start: 0.8215 (m) cc_final: 0.7572 (p) REVERT: E 21 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8713 (mt-10) REVERT: E 35 VAL cc_start: 0.8909 (t) cc_final: 0.8652 (p) REVERT: E 50 MET cc_start: 0.7185 (mmm) cc_final: 0.6960 (mpp) REVERT: E 84 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: E 213 ILE cc_start: 0.7294 (tt) cc_final: 0.5999 (tt) REVERT: G 59 GLN cc_start: 0.8575 (tt0) cc_final: 0.8136 (tp-100) REVERT: H 22 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7479 (mtpp) REVERT: H 121 LEU cc_start: 0.9027 (mp) cc_final: 0.8814 (mp) REVERT: H 125 LEU cc_start: 0.8763 (mt) cc_final: 0.8555 (tp) REVERT: I 27 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7233 (t0) REVERT: I 95 ASN cc_start: 0.6418 (m110) cc_final: 0.5802 (p0) REVERT: J 5 VAL cc_start: 0.8364 (t) cc_final: 0.8066 (t) REVERT: J 48 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8789 (ttp80) REVERT: J 56 LEU cc_start: 0.9449 (mt) cc_final: 0.9194 (mt) REVERT: J 60 PHE cc_start: 0.8306 (m-80) cc_final: 0.8063 (m-80) REVERT: K 66 VAL cc_start: 0.8198 (m) cc_final: 0.7484 (p) REVERT: K 132 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: L 40 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8646 (tp) REVERT: M 28 LYS cc_start: 0.8346 (tptt) cc_final: 0.8009 (tppt) REVERT: M 38 PHE cc_start: 0.8521 (m-80) cc_final: 0.8205 (m-80) REVERT: M 62 TYR cc_start: 0.7986 (m-80) cc_final: 0.6385 (m-80) REVERT: M 66 THR cc_start: 0.7417 (p) cc_final: 0.6205 (p) REVERT: M 113 ILE cc_start: 0.8069 (mt) cc_final: 0.7863 (mm) REVERT: N 36 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8237 (tttt) REVERT: N 94 ASP cc_start: 0.1635 (OUTLIER) cc_final: 0.1333 (m-30) REVERT: N 131 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.3727 (mt) REVERT: O 149 LYS cc_start: 0.0897 (OUTLIER) cc_final: -0.3583 (pttp) REVERT: O 363 THR cc_start: 0.6519 (OUTLIER) cc_final: 0.6097 (t) REVERT: O 395 LEU cc_start: 0.3487 (OUTLIER) cc_final: 0.3140 (mt) REVERT: O 469 ARG cc_start: 0.0112 (mtm180) cc_final: -0.0239 (mtp180) REVERT: O 471 LYS cc_start: 0.6770 (ptpt) cc_final: 0.6408 (mttm) REVERT: O 543 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7198 (mp) REVERT: O 551 ARG cc_start: 0.2732 (ttp80) cc_final: 0.0637 (tpt170) REVERT: O 602 TYR cc_start: 0.4567 (OUTLIER) cc_final: 0.3828 (t80) outliers start: 362 outliers final: 68 residues processed: 1761 average time/residue: 0.2351 time to fit residues: 658.2429 Evaluate side-chains 1021 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 924 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 0.0970 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 537 GLN A 538 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 634 ASN A 636 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 706 HIS A 730 GLN A 738 ASN A 753 ASN A 798 HIS A 926 GLN ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1180 ASN A1314 GLN A1323 HIS A1487 ASN A1503 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN A1633 GLN B 45 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 173 ASN B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 339 GLN B 361 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN B 683 ASN ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B 896 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS B 999 GLN B1008 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN B1100 GLN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 335 GLN E 54 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN G 59 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 124 ASN I 125 ASN J 26 GLN J 64 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS K 106 GLN N 50 GLN N 132 GLN N 170 HIS O 66 ASN O 173 HIS O 371 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 546 ASN O 547 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089290 restraints weight = 203671.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091142 restraints weight = 148318.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092069 restraints weight = 117181.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.093558 restraints weight = 100248.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094024 restraints weight = 87598.193| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1231 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1232 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.894 44443 Z= 0.396 Angle : 0.800 19.443 60029 Z= 0.423 Chirality : 0.048 0.270 6174 Planarity : 0.005 0.077 7686 Dihedral : 14.319 88.132 7179 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.04 % Favored : 95.67 % Rotamer: Outliers : 0.19 % Allowed : 4.50 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.37 (0.11), residues: 5522 helix: 1.03 (0.11), residues: 2212 sheet: -0.81 (0.17), residues: 774 loop : -1.19 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 111 TYR 0.046 0.003 TYR C 82 PHE 0.065 0.003 PHE O 189 TRP 0.059 0.003 TRP B 143 HIS 0.024 0.003 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.01143 (44412) covalent geometry : angle 0.79073 (60002) hydrogen bonds : bond 0.05298 ( 2132) hydrogen bonds : angle 5.78064 ( 6059) metal coordination : bond 0.00868 ( 22) metal coordination : angle 5.73147 ( 27) Misc. bond : bond 0.00542 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1058 time to evaluate : 1.539 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9603 (mt) cc_final: 0.9351 (mt) REVERT: A 134 TYR cc_start: 0.9215 (m-80) cc_final: 0.8942 (m-80) REVERT: A 188 TYR cc_start: 0.9492 (t80) cc_final: 0.9152 (t80) REVERT: A 331 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9171 (mm-30) REVERT: A 358 ASP cc_start: 0.9391 (m-30) cc_final: 0.9137 (t70) REVERT: A 472 MET cc_start: 0.8877 (mmp) cc_final: 0.8031 (mmt) REVERT: A 572 THR cc_start: 0.9320 (p) cc_final: 0.9113 (p) REVERT: A 578 TYR cc_start: 0.9372 (m-10) cc_final: 0.8856 (m-80) REVERT: A 597 LYS cc_start: 0.9188 (pttm) cc_final: 0.8952 (pttt) REVERT: A 600 MET cc_start: 0.8673 (ttt) cc_final: 0.8358 (ttt) REVERT: A 635 MET cc_start: 0.8941 (tmm) cc_final: 0.8471 (tmm) REVERT: A 675 SER cc_start: 0.9549 (m) cc_final: 0.9227 (p) REVERT: A 695 TYR cc_start: 0.8585 (m-80) cc_final: 0.8360 (m-80) REVERT: A 699 CYS cc_start: 0.8143 (p) cc_final: 0.7726 (p) REVERT: A 719 ILE cc_start: 0.9453 (mt) cc_final: 0.9217 (mt) REVERT: A 754 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8526 (mmmt) REVERT: A 755 ILE cc_start: 0.8898 (mt) cc_final: 0.8640 (mt) REVERT: A 766 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 771 PHE cc_start: 0.8987 (m-80) cc_final: 0.8689 (m-10) REVERT: A 780 ILE cc_start: 0.9392 (pt) cc_final: 0.8953 (pt) REVERT: A 782 ASP cc_start: 0.9167 (m-30) cc_final: 0.8939 (m-30) REVERT: A 830 MET cc_start: 0.9178 (mmp) cc_final: 0.8851 (mmm) REVERT: A 928 MET cc_start: 0.8328 (ttm) cc_final: 0.7955 (ttm) REVERT: A 947 LEU cc_start: 0.9185 (mm) cc_final: 0.8841 (mm) REVERT: A 952 LEU cc_start: 0.9186 (mm) cc_final: 0.8535 (mm) REVERT: A 977 MET cc_start: 0.8599 (ttt) cc_final: 0.7656 (tpt) REVERT: A 994 GLU cc_start: 0.9177 (mp0) cc_final: 0.8690 (mp0) REVERT: A 995 TYR cc_start: 0.9595 (t80) cc_final: 0.9118 (t80) REVERT: A 1018 TYR cc_start: 0.8493 (t80) cc_final: 0.7928 (t80) REVERT: A 1144 LEU cc_start: 0.9700 (tp) cc_final: 0.9216 (pp) REVERT: A 1183 GLU cc_start: 0.9575 (tp30) cc_final: 0.9311 (mm-30) REVERT: A 1192 SER cc_start: 0.9449 (m) cc_final: 0.9239 (p) REVERT: A 1238 MET cc_start: 0.8592 (mtm) cc_final: 0.8030 (mtt) REVERT: A 1305 GLU cc_start: 0.8205 (tp30) cc_final: 0.7923 (tp30) REVERT: A 1479 ASP cc_start: 0.9383 (t70) cc_final: 0.9123 (t0) REVERT: A 1530 TRP cc_start: 0.9231 (m-10) cc_final: 0.8718 (m-10) REVERT: A 1545 ASP cc_start: 0.8638 (t70) cc_final: 0.8258 (t0) REVERT: A 1575 ILE cc_start: 0.8642 (mp) cc_final: 0.8047 (mm) REVERT: A 1583 ASP cc_start: 0.9574 (m-30) cc_final: 0.9364 (m-30) REVERT: A 1587 ASP cc_start: 0.9708 (m-30) cc_final: 0.9245 (m-30) REVERT: A 1588 MET cc_start: 0.9640 (tpt) cc_final: 0.9287 (tpt) REVERT: A 1592 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8363 (tm-30) REVERT: A 1610 PHE cc_start: 0.9549 (m-10) cc_final: 0.9236 (m-80) REVERT: A 1628 ASP cc_start: 0.9557 (t70) cc_final: 0.9190 (t0) REVERT: A 1655 ASP cc_start: 0.9045 (t0) cc_final: 0.8838 (t0) REVERT: B 129 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8268 (tpt170) REVERT: B 215 MET cc_start: 0.7640 (mmm) cc_final: 0.7350 (mmm) REVERT: B 264 TRP cc_start: 0.8993 (t-100) cc_final: 0.8440 (t-100) REVERT: B 338 PHE cc_start: 0.8910 (m-80) cc_final: 0.8282 (m-80) REVERT: B 419 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9060 (mt-10) REVERT: B 448 ARG cc_start: 0.9451 (tpm170) cc_final: 0.9039 (tpm170) REVERT: B 461 MET cc_start: 0.9011 (tpp) cc_final: 0.8032 (mmt) REVERT: B 489 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 524 SER cc_start: 0.9294 (p) cc_final: 0.9074 (p) REVERT: B 575 HIS cc_start: 0.6999 (m90) cc_final: 0.5978 (m90) REVERT: B 591 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9204 (tptt) REVERT: B 625 GLU cc_start: 0.8605 (tt0) cc_final: 0.8213 (tp30) REVERT: B 641 TYR cc_start: 0.8757 (m-80) cc_final: 0.7855 (m-80) REVERT: B 672 MET cc_start: 0.8535 (mtm) cc_final: 0.7972 (ptp) REVERT: B 677 THR cc_start: 0.9018 (p) cc_final: 0.8358 (t) REVERT: B 680 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8814 (mt-10) REVERT: B 715 ASN cc_start: 0.9231 (m-40) cc_final: 0.8224 (m110) REVERT: B 726 MET cc_start: 0.8437 (ttp) cc_final: 0.7779 (ttp) REVERT: B 740 LYS cc_start: 0.9628 (pttm) cc_final: 0.9095 (ttpp) REVERT: B 742 TYR cc_start: 0.8798 (m-10) cc_final: 0.7547 (m-10) REVERT: B 782 ASP cc_start: 0.9068 (p0) cc_final: 0.8140 (p0) REVERT: B 787 MET cc_start: 0.8579 (ppp) cc_final: 0.8364 (ppp) REVERT: B 803 MET cc_start: 0.8608 (ttp) cc_final: 0.8057 (tmm) REVERT: B 904 LYS cc_start: 0.9456 (mtpt) cc_final: 0.9094 (mtpt) REVERT: B 923 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 1005 TYR cc_start: 0.8325 (m-10) cc_final: 0.8047 (m-10) REVERT: B 1034 GLN cc_start: 0.8798 (mt0) cc_final: 0.8470 (mp10) REVERT: B 1039 MET cc_start: 0.2546 (tmm) cc_final: 0.1540 (tmm) REVERT: B 1055 LEU cc_start: 0.9248 (mm) cc_final: 0.8712 (tp) REVERT: B 1074 MET cc_start: 0.9000 (mtt) cc_final: 0.8418 (mtp) REVERT: B 1077 ASP cc_start: 0.9374 (m-30) cc_final: 0.9038 (m-30) REVERT: B 1084 THR cc_start: 0.8839 (p) cc_final: 0.8440 (p) REVERT: B 1133 MET cc_start: 0.9213 (tpt) cc_final: 0.8970 (tpp) REVERT: B 1180 PHE cc_start: 0.8745 (t80) cc_final: 0.8111 (t80) REVERT: B 1184 TYR cc_start: 0.9321 (t80) cc_final: 0.9028 (t80) REVERT: C 56 LEU cc_start: 0.9713 (mp) cc_final: 0.9351 (mp) REVERT: C 67 PHE cc_start: 0.9730 (m-80) cc_final: 0.9366 (m-80) REVERT: C 74 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8985 (mm-30) REVERT: C 167 LEU cc_start: 0.9013 (mt) cc_final: 0.8810 (mt) REVERT: C 188 ASP cc_start: 0.8353 (t0) cc_final: 0.7781 (t0) REVERT: C 192 LEU cc_start: 0.9230 (tp) cc_final: 0.8948 (tt) REVERT: C 193 LEU cc_start: 0.9511 (mt) cc_final: 0.9294 (mt) REVERT: C 229 LEU cc_start: 0.8721 (tp) cc_final: 0.8438 (tp) REVERT: C 272 LYS cc_start: 0.9620 (tptt) cc_final: 0.9327 (tttp) REVERT: D 20 VAL cc_start: 0.7194 (t) cc_final: 0.6668 (t) REVERT: E 1 MET cc_start: 0.9145 (tmm) cc_final: 0.8894 (tmm) REVERT: E 18 THR cc_start: 0.8803 (m) cc_final: 0.8219 (p) REVERT: E 21 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8854 (mt-10) REVERT: E 22 MET cc_start: 0.9017 (ttm) cc_final: 0.8736 (ttt) REVERT: E 39 LEU cc_start: 0.9534 (tp) cc_final: 0.9252 (tp) REVERT: E 50 MET cc_start: 0.7636 (mmm) cc_final: 0.7345 (mpp) REVERT: E 58 MET cc_start: 0.8588 (mpp) cc_final: 0.8370 (mpp) REVERT: E 112 TYR cc_start: 0.9380 (p90) cc_final: 0.8873 (p90) REVERT: E 140 LEU cc_start: 0.9303 (mt) cc_final: 0.9044 (mt) REVERT: E 192 ARG cc_start: 0.8897 (ptp-110) cc_final: 0.8534 (ptp-170) REVERT: E 213 ILE cc_start: 0.8295 (tt) cc_final: 0.7443 (tp) REVERT: G 71 MET cc_start: 0.7866 (mmm) cc_final: 0.7444 (mmp) REVERT: G 172 ASP cc_start: 0.4311 (m-30) cc_final: 0.3860 (p0) REVERT: H 42 ILE cc_start: 0.9455 (pt) cc_final: 0.9157 (mp) REVERT: H 137 GLN cc_start: 0.9008 (mt0) cc_final: 0.8799 (mp10) REVERT: H 141 TYR cc_start: 0.8517 (m-80) cc_final: 0.8134 (m-80) REVERT: I 56 PHE cc_start: 0.8826 (m-80) cc_final: 0.8318 (m-80) REVERT: J 5 VAL cc_start: 0.9178 (t) cc_final: 0.8865 (t) REVERT: K 91 TYR cc_start: 0.8211 (p90) cc_final: 0.7682 (p90) REVERT: K 99 ASN cc_start: 0.9487 (m-40) cc_final: 0.9117 (m-40) REVERT: K 125 MET cc_start: 0.7788 (ptp) cc_final: 0.6888 (ptt) REVERT: K 135 PHE cc_start: 0.9448 (t80) cc_final: 0.8720 (t80) REVERT: K 138 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8537 (mmmt) REVERT: L 40 LEU cc_start: 0.8781 (tp) cc_final: 0.8476 (tt) REVERT: L 46 VAL cc_start: 0.8026 (t) cc_final: 0.7665 (m) REVERT: L 53 HIS cc_start: 0.8913 (t70) cc_final: 0.8488 (t70) REVERT: L 55 ILE cc_start: 0.9661 (mt) cc_final: 0.9424 (mm) REVERT: M 38 PHE cc_start: 0.9347 (m-80) cc_final: 0.9035 (m-80) REVERT: M 52 VAL cc_start: 0.8064 (t) cc_final: 0.7767 (t) REVERT: N 90 MET cc_start: 0.9350 (tpt) cc_final: 0.9051 (tpt) REVERT: N 107 MET cc_start: 0.1369 (mmt) cc_final: 0.1012 (mpp) REVERT: O 125 TRP cc_start: 0.7531 (p-90) cc_final: 0.6514 (p-90) REVERT: O 467 MET cc_start: 0.3336 (mmp) cc_final: 0.3018 (mmp) REVERT: O 505 PHE cc_start: 0.5137 (t80) cc_final: 0.3603 (t80) REVERT: O 508 ARG cc_start: 0.6627 (ptp-170) cc_final: 0.5466 (tmt-80) REVERT: O 527 MET cc_start: 0.5526 (tpt) cc_final: 0.5281 (tmm) outliers start: 8 outliers final: 1 residues processed: 1064 average time/residue: 0.2407 time to fit residues: 410.2285 Evaluate side-chains 807 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 806 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 318 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 452 optimal weight: 9.9990 chunk 494 optimal weight: 8.9990 chunk 549 optimal weight: 30.0000 chunk 314 optimal weight: 9.9990 chunk 471 optimal weight: 0.0670 chunk 292 optimal weight: 30.0000 chunk 407 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 538 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN A 671 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 880 GLN A 887 ASN A 906 GLN A 942 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN A1443 GLN A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN E 8 ASN E 114 ASN E 146 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN H 35 GLN K 70 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 478 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080630 restraints weight = 191636.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082078 restraints weight = 145200.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082766 restraints weight = 118286.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083759 restraints weight = 103645.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084193 restraints weight = 92321.514| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.947 44443 Z= 0.408 Angle : 0.748 18.594 60029 Z= 0.399 Chirality : 0.046 0.265 6174 Planarity : 0.006 0.248 7686 Dihedral : 14.419 88.176 7179 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.06 (0.11), residues: 5522 helix: 1.30 (0.11), residues: 2240 sheet: -0.49 (0.18), residues: 766 loop : -0.93 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A1003 TYR 0.040 0.003 TYR C 82 PHE 0.066 0.003 PHE O 189 TRP 0.069 0.003 TRP B 143 HIS 0.011 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.01166 (44412) covalent geometry : angle 0.73956 (60002) hydrogen bonds : bond 0.04610 ( 2132) hydrogen bonds : angle 5.41201 ( 6059) metal coordination : bond 0.01292 ( 22) metal coordination : angle 5.40388 ( 27) Misc. bond : bond 0.02612 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 966 time to evaluate : 1.168 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: 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: 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: 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: 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: 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: 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: A 10 GLU cc_start: 0.9536 (pp20) cc_final: 0.9322 (pm20) REVERT: A 15 ASP cc_start: 0.9115 (m-30) cc_final: 0.8870 (m-30) REVERT: A 16 PHE cc_start: 0.9084 (m-10) cc_final: 0.8822 (m-10) REVERT: A 134 TYR cc_start: 0.9247 (m-80) cc_final: 0.8821 (m-80) REVERT: A 188 TYR cc_start: 0.9470 (t80) cc_final: 0.8978 (t80) REVERT: A 205 ARG cc_start: 0.9182 (mmp-170) cc_final: 0.8725 (tpm170) REVERT: A 471 MET cc_start: 0.9723 (mtt) cc_final: 0.9510 (mpp) REVERT: A 472 MET cc_start: 0.8974 (mmp) cc_final: 0.8466 (mmp) REVERT: A 489 ASN cc_start: 0.9222 (m-40) cc_final: 0.9014 (m-40) REVERT: A 505 LEU cc_start: 0.9549 (mt) cc_final: 0.9152 (mp) REVERT: A 578 TYR cc_start: 0.9459 (m-10) cc_final: 0.8913 (m-80) REVERT: A 604 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9102 (tptp) REVERT: A 613 THR cc_start: 0.9660 (p) cc_final: 0.8987 (t) REVERT: A 614 LEU cc_start: 0.9314 (mt) cc_final: 0.8969 (mt) REVERT: A 615 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8574 (mmm-85) REVERT: A 633 MET cc_start: 0.7885 (mtp) cc_final: 0.7675 (mtp) REVERT: A 635 MET cc_start: 0.9147 (tmm) cc_final: 0.8711 (ppp) REVERT: A 658 LEU cc_start: 0.9801 (mt) cc_final: 0.9438 (mt) REVERT: A 675 SER cc_start: 0.9570 (m) cc_final: 0.9203 (p) REVERT: A 691 GLN cc_start: 0.9393 (pt0) cc_final: 0.8759 (pt0) REVERT: A 695 TYR cc_start: 0.9282 (m-80) cc_final: 0.8507 (m-80) REVERT: A 699 CYS cc_start: 0.8457 (p) cc_final: 0.7754 (p) REVERT: A 754 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8857 (mmmt) REVERT: A 755 ILE cc_start: 0.9103 (mt) cc_final: 0.8643 (mt) REVERT: A 760 TRP cc_start: 0.9017 (m100) cc_final: 0.8584 (m100) REVERT: A 780 ILE cc_start: 0.9359 (pt) cc_final: 0.8988 (pt) REVERT: A 801 TYR cc_start: 0.7927 (m-10) cc_final: 0.7658 (m-10) REVERT: A 830 MET cc_start: 0.9205 (mmp) cc_final: 0.8931 (mmm) REVERT: A 928 MET cc_start: 0.8629 (ttm) cc_final: 0.8352 (ttm) REVERT: A 934 LYS cc_start: 0.9397 (tptm) cc_final: 0.8852 (mmmm) REVERT: A 939 ASN cc_start: 0.9477 (m110) cc_final: 0.8907 (t0) REVERT: A 994 GLU cc_start: 0.9184 (mp0) cc_final: 0.8896 (mp0) REVERT: A 995 TYR cc_start: 0.9618 (t80) cc_final: 0.9307 (t80) REVERT: A 1000 MET cc_start: 0.8896 (mtm) cc_final: 0.8581 (mpp) REVERT: A 1018 TYR cc_start: 0.8671 (t80) cc_final: 0.8144 (t80) REVERT: A 1079 LYS cc_start: 0.8465 (tttp) cc_final: 0.8198 (ptmt) REVERT: A 1121 ASP cc_start: 0.8479 (p0) cc_final: 0.7885 (p0) REVERT: A 1192 SER cc_start: 0.9500 (m) cc_final: 0.9263 (p) REVERT: A 1238 MET cc_start: 0.8697 (mtm) cc_final: 0.8046 (mtt) REVERT: A 1306 TYR cc_start: 0.7939 (m-80) cc_final: 0.6965 (m-80) REVERT: A 1479 ASP cc_start: 0.9453 (t70) cc_final: 0.9210 (p0) REVERT: A 1530 TRP cc_start: 0.9292 (m-10) cc_final: 0.8638 (m-10) REVERT: A 1545 ASP cc_start: 0.8843 (t70) cc_final: 0.8424 (t0) REVERT: A 1610 PHE cc_start: 0.9549 (m-10) cc_final: 0.9263 (m-10) REVERT: A 1616 GLU cc_start: 0.8454 (pp20) cc_final: 0.8168 (pp20) REVERT: A 1621 PHE cc_start: 0.9326 (m-80) cc_final: 0.9038 (m-10) REVERT: A 1647 ASN cc_start: 0.9163 (t0) cc_final: 0.8582 (t0) REVERT: A 1655 ASP cc_start: 0.9028 (t0) cc_final: 0.8798 (t0) REVERT: B 175 MET cc_start: 0.8985 (tpp) cc_final: 0.7994 (tpp) REVERT: B 215 MET cc_start: 0.8106 (mmm) cc_final: 0.7044 (mmm) REVERT: B 248 ASN cc_start: 0.8396 (t0) cc_final: 0.8015 (p0) REVERT: B 373 MET cc_start: 0.9663 (tpt) cc_final: 0.9344 (tpp) REVERT: B 380 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7857 (ptpp) REVERT: B 392 ASP cc_start: 0.7644 (m-30) cc_final: 0.5912 (m-30) REVERT: B 415 GLU cc_start: 0.9104 (tp30) cc_final: 0.8877 (tp30) REVERT: B 416 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9169 (mmtt) REVERT: B 419 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9132 (mt-10) REVERT: B 446 MET cc_start: 0.8643 (mtt) cc_final: 0.8361 (mtp) REVERT: B 500 PHE cc_start: 0.9457 (m-80) cc_final: 0.9129 (m-80) REVERT: B 516 THR cc_start: 0.9532 (p) cc_final: 0.9211 (p) REVERT: B 641 TYR cc_start: 0.8727 (m-80) cc_final: 0.7996 (m-80) REVERT: B 649 MET cc_start: 0.8731 (mpp) cc_final: 0.8516 (mpp) REVERT: B 672 MET cc_start: 0.8737 (mtm) cc_final: 0.8136 (ptp) REVERT: B 677 THR cc_start: 0.9259 (p) cc_final: 0.8937 (p) REVERT: B 703 LEU cc_start: 0.9721 (mm) cc_final: 0.9345 (mm) REVERT: B 715 ASN cc_start: 0.9168 (m-40) cc_final: 0.8475 (m-40) REVERT: B 740 LYS cc_start: 0.9599 (pttm) cc_final: 0.9024 (ttpp) REVERT: B 742 TYR cc_start: 0.9082 (m-10) cc_final: 0.7998 (m-10) REVERT: B 778 TYR cc_start: 0.7747 (t80) cc_final: 0.7536 (t80) REVERT: B 779 THR cc_start: 0.9108 (p) cc_final: 0.8675 (t) REVERT: B 782 ASP cc_start: 0.9181 (p0) cc_final: 0.7922 (p0) REVERT: B 803 MET cc_start: 0.8913 (ttp) cc_final: 0.8081 (tmm) REVERT: B 917 PHE cc_start: 0.8539 (m-80) cc_final: 0.8169 (m-80) REVERT: B 923 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 931 TRP cc_start: 0.9441 (t-100) cc_final: 0.8452 (t-100) REVERT: B 933 THR cc_start: 0.8375 (t) cc_final: 0.8100 (t) REVERT: B 935 ASP cc_start: 0.9489 (m-30) cc_final: 0.8517 (t0) REVERT: B 954 PHE cc_start: 0.9024 (m-10) cc_final: 0.8818 (m-80) REVERT: B 959 THR cc_start: 0.9244 (p) cc_final: 0.8438 (p) REVERT: B 988 GLU cc_start: 0.9447 (pm20) cc_final: 0.9230 (pm20) REVERT: B 1013 MET cc_start: 0.8953 (mmm) cc_final: 0.8312 (mmm) REVERT: B 1034 GLN cc_start: 0.8918 (mt0) cc_final: 0.8558 (mp10) REVERT: B 1039 MET cc_start: 0.3762 (tmm) cc_final: 0.3123 (tmm) REVERT: B 1074 MET cc_start: 0.8925 (mtt) cc_final: 0.8537 (mtp) REVERT: B 1084 THR cc_start: 0.9073 (p) cc_final: 0.8717 (p) REVERT: B 1180 PHE cc_start: 0.9240 (t80) cc_final: 0.8675 (t80) REVERT: B 1196 LEU cc_start: 0.9399 (mm) cc_final: 0.9105 (mm) REVERT: C 56 LEU cc_start: 0.9762 (mp) cc_final: 0.9347 (mt) REVERT: C 67 PHE cc_start: 0.9678 (m-80) cc_final: 0.9330 (m-80) REVERT: C 71 MET cc_start: 0.9338 (mmm) cc_final: 0.9047 (mmm) REVERT: C 129 GLU cc_start: 0.9221 (pm20) cc_final: 0.8844 (tp30) REVERT: C 154 LYS cc_start: 0.9307 (mptt) cc_final: 0.8982 (mmmt) REVERT: C 188 ASP cc_start: 0.8544 (t0) cc_final: 0.8032 (t0) REVERT: C 191 ILE cc_start: 0.9581 (mt) cc_final: 0.9352 (mm) REVERT: C 207 HIS cc_start: 0.8888 (m90) cc_final: 0.8656 (m90) REVERT: C 229 LEU cc_start: 0.8794 (tp) cc_final: 0.8519 (tp) REVERT: C 272 LYS cc_start: 0.9616 (tptt) cc_final: 0.9373 (tttp) REVERT: C 314 PHE cc_start: 0.9645 (t80) cc_final: 0.9439 (t80) REVERT: D 29 GLN cc_start: 0.9136 (mp10) cc_final: 0.8777 (pm20) REVERT: D 94 ARG cc_start: 0.9466 (ptt-90) cc_final: 0.9027 (ttp80) REVERT: E 1 MET cc_start: 0.9374 (tmm) cc_final: 0.9149 (tmm) REVERT: E 4 GLU cc_start: 0.9409 (tp30) cc_final: 0.9179 (tp30) REVERT: E 18 THR cc_start: 0.8987 (m) cc_final: 0.8463 (p) REVERT: E 21 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8855 (mt-10) REVERT: E 22 MET cc_start: 0.8959 (ttm) cc_final: 0.8635 (ttt) REVERT: E 50 MET cc_start: 0.7693 (mmm) cc_final: 0.7262 (mpp) REVERT: E 82 PHE cc_start: 0.9284 (m-80) cc_final: 0.8810 (m-80) REVERT: E 112 TYR cc_start: 0.9358 (p90) cc_final: 0.8569 (p90) REVERT: E 168 TYR cc_start: 0.9111 (m-80) cc_final: 0.8600 (m-80) REVERT: E 172 GLU cc_start: 0.8626 (pm20) cc_final: 0.8305 (pm20) REVERT: E 179 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7914 (mm-40) REVERT: E 213 ILE cc_start: 0.8336 (tt) cc_final: 0.7280 (tp) REVERT: G 40 ARG cc_start: 0.9616 (tpt90) cc_final: 0.9348 (tpt90) REVERT: G 52 MET cc_start: 0.9463 (mmm) cc_final: 0.9148 (mmm) REVERT: G 71 MET cc_start: 0.7977 (mmm) cc_final: 0.7620 (mmm) REVERT: G 144 HIS cc_start: 0.5369 (p-80) cc_final: 0.5031 (p-80) REVERT: G 166 TRP cc_start: 0.6553 (m-10) cc_final: 0.6330 (m-10) REVERT: G 172 ASP cc_start: 0.4487 (m-30) cc_final: 0.3902 (p0) REVERT: H 42 ILE cc_start: 0.9510 (pt) cc_final: 0.9008 (mp) REVERT: H 141 TYR cc_start: 0.8427 (m-80) cc_final: 0.8167 (m-80) REVERT: I 71 LEU cc_start: 0.9038 (mt) cc_final: 0.8750 (tp) REVERT: J 1 MET cc_start: 0.9040 (mmm) cc_final: 0.8830 (mmm) REVERT: J 5 VAL cc_start: 0.9396 (t) cc_final: 0.9111 (t) REVERT: J 16 ASP cc_start: 0.8801 (p0) cc_final: 0.8352 (p0) REVERT: J 41 LEU cc_start: 0.8818 (mt) cc_final: 0.8556 (mp) REVERT: J 49 MET cc_start: 0.9472 (mmm) cc_final: 0.8972 (mmm) REVERT: J 58 GLU cc_start: 0.9533 (mm-30) cc_final: 0.8517 (tp30) REVERT: K 69 ASP cc_start: 0.8739 (p0) cc_final: 0.8413 (p0) REVERT: K 91 TYR cc_start: 0.8761 (p90) cc_final: 0.8260 (p90) REVERT: K 101 LEU cc_start: 0.9191 (tp) cc_final: 0.8981 (tp) REVERT: K 125 MET cc_start: 0.8596 (ptp) cc_final: 0.7731 (ptt) REVERT: L 30 ILE cc_start: 0.8816 (mm) cc_final: 0.8599 (mm) REVERT: L 33 GLU cc_start: 0.9598 (tp30) cc_final: 0.9217 (tm-30) REVERT: M 52 VAL cc_start: 0.8038 (t) cc_final: 0.7751 (t) REVERT: N 34 HIS cc_start: 0.8892 (t-90) cc_final: 0.8541 (t70) REVERT: O 125 TRP cc_start: 0.7832 (p-90) cc_final: 0.7041 (p-90) REVERT: O 467 MET cc_start: 0.3018 (mmp) cc_final: 0.2696 (mmt) REVERT: O 505 PHE cc_start: 0.4853 (t80) cc_final: 0.3488 (t80) REVERT: O 508 ARG cc_start: 0.6603 (ptp-170) cc_final: 0.5491 (tmt-80) REVERT: O 525 MET cc_start: -0.1979 (tpt) cc_final: -0.2442 (tpt) REVERT: O 527 MET cc_start: 0.5566 (tpt) cc_final: 0.5297 (tmm) outliers start: 5 outliers final: 1 residues processed: 970 average time/residue: 0.2379 time to fit residues: 370.6370 Evaluate side-chains 761 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 760 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 165 optimal weight: 8.9990 chunk 410 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 539 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 396 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080064 restraints weight = 191522.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081080 restraints weight = 143838.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082460 restraints weight = 119698.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.082974 restraints weight = 102120.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.083454 restraints weight = 92205.072| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.940 44443 Z= 0.377 Angle : 0.676 19.137 60029 Z= 0.355 Chirality : 0.045 0.321 6174 Planarity : 0.005 0.109 7686 Dihedral : 14.378 83.350 7179 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.95 % Favored : 95.85 % Rotamer: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.14 (0.11), residues: 5522 helix: 1.37 (0.11), residues: 2251 sheet: -0.41 (0.17), residues: 777 loop : -0.90 (0.13), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 709 TYR 0.029 0.002 TYR B 232 PHE 0.039 0.002 PHE O 189 TRP 0.056 0.002 TRP B 143 HIS 0.010 0.002 HIS G 150 Details of bonding type rmsd covalent geometry : bond 0.01125 (44412) covalent geometry : angle 0.66725 (60002) hydrogen bonds : bond 0.04014 ( 2132) hydrogen bonds : angle 5.13961 ( 6059) metal coordination : bond 0.00994 ( 22) metal coordination : angle 5.23676 ( 27) Misc. bond : bond 0.00558 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 936 time to evaluate : 1.259 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: 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: 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: 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: 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: 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: 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: A 134 TYR cc_start: 0.9167 (m-80) cc_final: 0.8945 (m-80) REVERT: A 331 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9209 (mm-30) REVERT: A 472 MET cc_start: 0.8604 (mmp) cc_final: 0.8329 (mmp) REVERT: A 505 LEU cc_start: 0.9537 (mt) cc_final: 0.9042 (mp) REVERT: A 578 TYR cc_start: 0.9456 (m-10) cc_final: 0.8949 (m-80) REVERT: A 590 ASN cc_start: 0.8537 (m-40) cc_final: 0.8337 (m-40) REVERT: A 595 LEU cc_start: 0.9588 (mt) cc_final: 0.9115 (mp) REVERT: A 597 LYS cc_start: 0.8418 (pttm) cc_final: 0.8023 (pttt) REVERT: A 604 LYS cc_start: 0.9265 (mmmt) cc_final: 0.9050 (tptp) REVERT: A 613 THR cc_start: 0.9671 (p) cc_final: 0.9281 (t) REVERT: A 614 LEU cc_start: 0.9299 (mt) cc_final: 0.9070 (mt) REVERT: A 635 MET cc_start: 0.9438 (tmm) cc_final: 0.9052 (tmm) REVERT: A 658 LEU cc_start: 0.9785 (mt) cc_final: 0.9412 (mt) REVERT: A 671 GLN cc_start: 0.8563 (mt0) cc_final: 0.7957 (mt0) REVERT: A 675 SER cc_start: 0.9585 (m) cc_final: 0.9314 (p) REVERT: A 691 GLN cc_start: 0.9338 (pt0) cc_final: 0.8995 (pt0) REVERT: A 695 TYR cc_start: 0.9199 (m-80) cc_final: 0.8409 (m-80) REVERT: A 699 CYS cc_start: 0.8171 (p) cc_final: 0.7369 (p) REVERT: A 715 LEU cc_start: 0.8993 (mt) cc_final: 0.8754 (mt) REVERT: A 744 MET cc_start: 0.8628 (mmp) cc_final: 0.8320 (mmm) REVERT: A 754 LYS cc_start: 0.9259 (mmpt) cc_final: 0.8974 (mmmt) REVERT: A 755 ILE cc_start: 0.9174 (mt) cc_final: 0.8794 (mt) REVERT: A 760 TRP cc_start: 0.8917 (m100) cc_final: 0.8414 (m100) REVERT: A 780 ILE cc_start: 0.9348 (pt) cc_final: 0.8985 (pt) REVERT: A 782 ASP cc_start: 0.9059 (m-30) cc_final: 0.8556 (m-30) REVERT: A 826 PHE cc_start: 0.8934 (t80) cc_final: 0.8671 (t80) REVERT: A 926 GLN cc_start: 0.8891 (mt0) cc_final: 0.8647 (mt0) REVERT: A 934 LYS cc_start: 0.9403 (tptm) cc_final: 0.8864 (mmmm) REVERT: A 977 MET cc_start: 0.8668 (ttt) cc_final: 0.7811 (tpt) REVERT: A 986 PHE cc_start: 0.8957 (m-80) cc_final: 0.8614 (m-80) REVERT: A 994 GLU cc_start: 0.9142 (mp0) cc_final: 0.8576 (mp0) REVERT: A 995 TYR cc_start: 0.9588 (t80) cc_final: 0.9271 (t80) REVERT: A 1000 MET cc_start: 0.8939 (mtm) cc_final: 0.8578 (mtp) REVERT: A 1018 TYR cc_start: 0.8702 (t80) cc_final: 0.8225 (t80) REVERT: A 1021 ARG cc_start: 0.9200 (mmt180) cc_final: 0.8539 (mmt180) REVERT: A 1079 LYS cc_start: 0.8338 (tttp) cc_final: 0.8111 (ptmt) REVERT: A 1121 ASP cc_start: 0.8551 (p0) cc_final: 0.7952 (p0) REVERT: A 1195 GLU cc_start: 0.9589 (tm-30) cc_final: 0.9085 (tp30) REVERT: A 1203 ASN cc_start: 0.9733 (t0) cc_final: 0.9530 (t0) REVERT: A 1320 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8112 (pp30) REVERT: A 1332 GLU cc_start: 0.9686 (pt0) cc_final: 0.9445 (pp20) REVERT: A 1545 ASP cc_start: 0.8701 (t70) cc_final: 0.8264 (t0) REVERT: A 1610 PHE cc_start: 0.9459 (m-10) cc_final: 0.9102 (m-80) REVERT: A 1616 GLU cc_start: 0.8474 (pp20) cc_final: 0.8271 (pp20) REVERT: A 1647 ASN cc_start: 0.9270 (t0) cc_final: 0.9047 (t0) REVERT: A 1655 ASP cc_start: 0.9305 (t0) cc_final: 0.8818 (t0) REVERT: B 25 PHE cc_start: 0.9289 (m-80) cc_final: 0.9001 (m-80) REVERT: B 158 CYS cc_start: 0.8411 (m) cc_final: 0.7951 (m) REVERT: B 215 MET cc_start: 0.8143 (mmm) cc_final: 0.7246 (mmm) REVERT: B 373 MET cc_start: 0.9650 (tpt) cc_final: 0.9301 (mpp) REVERT: B 392 ASP cc_start: 0.7797 (m-30) cc_final: 0.6400 (m-30) REVERT: B 398 GLN cc_start: 0.9233 (pt0) cc_final: 0.8558 (pt0) REVERT: B 407 PHE cc_start: 0.9347 (m-80) cc_final: 0.9071 (m-80) REVERT: B 419 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9110 (mt-10) REVERT: B 500 PHE cc_start: 0.9515 (m-80) cc_final: 0.9131 (m-80) REVERT: B 591 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9154 (tptp) REVERT: B 641 TYR cc_start: 0.8693 (m-80) cc_final: 0.7905 (m-80) REVERT: B 672 MET cc_start: 0.8706 (mtm) cc_final: 0.8255 (ptp) REVERT: B 703 LEU cc_start: 0.9701 (mm) cc_final: 0.9378 (mm) REVERT: B 715 ASN cc_start: 0.9145 (m-40) cc_final: 0.8403 (m-40) REVERT: B 716 MET cc_start: 0.9220 (mtm) cc_final: 0.8870 (mtm) REVERT: B 723 LYS cc_start: 0.9633 (mtmt) cc_final: 0.9322 (mttt) REVERT: B 728 THR cc_start: 0.9449 (m) cc_final: 0.8770 (p) REVERT: B 742 TYR cc_start: 0.8961 (m-10) cc_final: 0.8415 (m-10) REVERT: B 782 ASP cc_start: 0.9120 (p0) cc_final: 0.8103 (p0) REVERT: B 904 LYS cc_start: 0.9519 (mtpt) cc_final: 0.9031 (ttmm) REVERT: B 923 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 959 THR cc_start: 0.9116 (p) cc_final: 0.8752 (p) REVERT: B 988 GLU cc_start: 0.9398 (pm20) cc_final: 0.9152 (pm20) REVERT: B 1005 TYR cc_start: 0.8743 (m-10) cc_final: 0.8361 (m-10) REVERT: B 1013 MET cc_start: 0.8614 (mmm) cc_final: 0.8292 (tpt) REVERT: B 1034 GLN cc_start: 0.8998 (mt0) cc_final: 0.8325 (pm20) REVERT: B 1039 MET cc_start: 0.3947 (tmm) cc_final: 0.3620 (tmm) REVERT: B 1054 SER cc_start: 0.9361 (p) cc_final: 0.9014 (t) REVERT: B 1074 MET cc_start: 0.8934 (mtt) cc_final: 0.8703 (mmm) REVERT: B 1077 ASP cc_start: 0.9512 (m-30) cc_final: 0.9208 (m-30) REVERT: B 1084 THR cc_start: 0.9161 (p) cc_final: 0.8816 (p) REVERT: B 1092 LEU cc_start: 0.9474 (mm) cc_final: 0.9265 (mm) REVERT: B 1133 MET cc_start: 0.9277 (tpt) cc_final: 0.8793 (ppp) REVERT: B 1180 PHE cc_start: 0.9274 (t80) cc_final: 0.8443 (t80) REVERT: B 1196 LEU cc_start: 0.9454 (mm) cc_final: 0.9111 (mm) REVERT: C 56 LEU cc_start: 0.9774 (mp) cc_final: 0.9329 (mp) REVERT: C 63 ILE cc_start: 0.9333 (mp) cc_final: 0.9071 (mp) REVERT: C 67 PHE cc_start: 0.9666 (m-80) cc_final: 0.9362 (m-80) REVERT: C 74 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9144 (mp0) REVERT: C 154 LYS cc_start: 0.9309 (mptt) cc_final: 0.8918 (mmmt) REVERT: C 188 ASP cc_start: 0.8728 (t0) cc_final: 0.8186 (t0) REVERT: C 191 ILE cc_start: 0.9570 (mt) cc_final: 0.9312 (mm) REVERT: C 192 LEU cc_start: 0.9428 (tp) cc_final: 0.9023 (tt) REVERT: C 229 LEU cc_start: 0.8725 (tp) cc_final: 0.8503 (tp) REVERT: C 272 LYS cc_start: 0.9628 (tptt) cc_final: 0.9289 (tptm) REVERT: C 290 LYS cc_start: 0.9615 (mmpt) cc_final: 0.9342 (mmpt) REVERT: D 94 ARG cc_start: 0.9318 (ptt-90) cc_final: 0.8932 (ttp80) REVERT: E 1 MET cc_start: 0.9410 (tmm) cc_final: 0.9190 (tmm) REVERT: E 18 THR cc_start: 0.8985 (m) cc_final: 0.8483 (p) REVERT: E 21 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8906 (mt-10) REVERT: E 22 MET cc_start: 0.9011 (ttm) cc_final: 0.8689 (ttt) REVERT: E 50 MET cc_start: 0.7721 (mmm) cc_final: 0.7266 (mpp) REVERT: E 57 MET cc_start: 0.7067 (ptt) cc_final: 0.6731 (ptt) REVERT: E 58 MET cc_start: 0.8910 (mpp) cc_final: 0.8427 (mpp) REVERT: E 82 PHE cc_start: 0.9275 (m-80) cc_final: 0.8785 (m-80) REVERT: E 112 TYR cc_start: 0.9413 (p90) cc_final: 0.8713 (p90) REVERT: E 168 TYR cc_start: 0.9188 (m-80) cc_final: 0.8661 (m-80) REVERT: E 179 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8027 (mm-40) REVERT: E 192 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8917 (ttp-110) REVERT: E 213 ILE cc_start: 0.8319 (tt) cc_final: 0.7385 (tp) REVERT: F 137 TYR cc_start: 0.8332 (m-80) cc_final: 0.7368 (t80) REVERT: G 52 MET cc_start: 0.9487 (mmm) cc_final: 0.9205 (mmt) REVERT: G 71 MET cc_start: 0.8045 (mmm) cc_final: 0.7695 (mmm) REVERT: H 42 ILE cc_start: 0.9492 (pt) cc_final: 0.8871 (mp) REVERT: H 95 TYR cc_start: 0.9084 (t80) cc_final: 0.8597 (t80) REVERT: H 97 MET cc_start: 0.8339 (mtm) cc_final: 0.7081 (mtm) REVERT: H 123 MET cc_start: 0.7417 (ptp) cc_final: 0.7203 (ppp) REVERT: H 141 TYR cc_start: 0.8375 (m-80) cc_final: 0.8098 (m-80) REVERT: I 71 LEU cc_start: 0.9101 (mt) cc_final: 0.8865 (tp) REVERT: J 5 VAL cc_start: 0.9363 (t) cc_final: 0.9018 (t) REVERT: J 16 ASP cc_start: 0.8854 (p0) cc_final: 0.8491 (p0) REVERT: J 49 MET cc_start: 0.9469 (mmm) cc_final: 0.9162 (mmm) REVERT: J 58 GLU cc_start: 0.9524 (mm-30) cc_final: 0.8796 (tp30) REVERT: K 50 LEU cc_start: 0.9059 (mp) cc_final: 0.8638 (tt) REVERT: K 69 ASP cc_start: 0.8767 (p0) cc_final: 0.8472 (p0) REVERT: K 91 TYR cc_start: 0.8808 (p90) cc_final: 0.8493 (p90) REVERT: K 99 ASN cc_start: 0.8932 (p0) cc_final: 0.8614 (p0) REVERT: K 101 LEU cc_start: 0.9098 (tp) cc_final: 0.8764 (tp) REVERT: K 125 MET cc_start: 0.8870 (ptp) cc_final: 0.7954 (ptt) REVERT: K 135 PHE cc_start: 0.9483 (t80) cc_final: 0.8720 (t80) REVERT: L 33 GLU cc_start: 0.9569 (tp30) cc_final: 0.9139 (tm-30) REVERT: M 38 PHE cc_start: 0.9192 (m-80) cc_final: 0.8885 (m-80) REVERT: N 34 HIS cc_start: 0.8842 (t-90) cc_final: 0.8493 (t70) REVERT: N 110 LEU cc_start: 0.9643 (mt) cc_final: 0.9437 (mm) REVERT: O 125 TRP cc_start: 0.7905 (p-90) cc_final: 0.6509 (p-90) REVERT: O 132 THR cc_start: -0.3515 (m) cc_final: -0.3782 (p) REVERT: O 396 MET cc_start: 0.6895 (mmm) cc_final: 0.6668 (mmm) REVERT: O 467 MET cc_start: 0.2999 (mmp) cc_final: 0.2636 (mmt) REVERT: O 505 PHE cc_start: 0.4730 (t80) cc_final: 0.3401 (t80) REVERT: O 508 ARG cc_start: 0.6837 (ptp-170) cc_final: 0.5735 (tmt-80) REVERT: O 525 MET cc_start: -0.1647 (tpt) cc_final: -0.2361 (tpt) REVERT: O 527 MET cc_start: 0.5650 (tpt) cc_final: 0.5382 (tmm) outliers start: 3 outliers final: 1 residues processed: 939 average time/residue: 0.2474 time to fit residues: 378.4227 Evaluate side-chains 759 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 757 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 433 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 0.0570 chunk 436 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 393 optimal weight: 20.0000 chunk 340 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 417 optimal weight: 9.9990 chunk 552 optimal weight: 20.0000 overall best weight: 4.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 560 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN A1180 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 248 ASN B 462 GLN B 473 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 99 HIS C 207 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS M 16 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076452 restraints weight = 193218.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.075948 restraints weight = 158042.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076769 restraints weight = 128695.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077618 restraints weight = 110388.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.077992 restraints weight = 99724.382| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.937 44443 Z= 0.436 Angle : 0.791 18.615 60029 Z= 0.414 Chirality : 0.046 0.353 6174 Planarity : 0.006 0.085 7686 Dihedral : 14.530 83.829 7179 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.11), residues: 5522 helix: 1.06 (0.11), residues: 2282 sheet: -0.40 (0.18), residues: 757 loop : -1.08 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG G 40 TYR 0.028 0.003 TYR A1302 PHE 0.045 0.003 PHE O 189 TRP 0.077 0.003 TRP B 143 HIS 0.012 0.003 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.01206 (44412) covalent geometry : angle 0.77727 (60002) hydrogen bonds : bond 0.04812 ( 2132) hydrogen bonds : angle 5.38934 ( 6059) metal coordination : bond 0.01623 ( 22) metal coordination : angle 6.98794 ( 27) Misc. bond : bond 0.00970 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 871 time to evaluate : 1.644 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: 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: 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: 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: 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: 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: 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: A 16 PHE cc_start: 0.9166 (m-10) cc_final: 0.8800 (m-10) REVERT: A 130 ILE cc_start: 0.9696 (mt) cc_final: 0.9345 (mp) REVERT: A 134 TYR cc_start: 0.9277 (m-80) cc_final: 0.9051 (m-80) REVERT: A 331 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9102 (mm-30) REVERT: A 472 MET cc_start: 0.8351 (mmp) cc_final: 0.7700 (mmt) REVERT: A 481 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8104 (ttp80) REVERT: A 520 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.7941 (mtt-85) REVERT: A 578 TYR cc_start: 0.9439 (m-10) cc_final: 0.8863 (m-80) REVERT: A 585 ASP cc_start: 0.8968 (m-30) cc_final: 0.8738 (m-30) REVERT: A 613 THR cc_start: 0.9687 (p) cc_final: 0.9010 (t) REVERT: A 614 LEU cc_start: 0.9373 (mt) cc_final: 0.8965 (mt) REVERT: A 615 ARG cc_start: 0.9187 (mmm-85) cc_final: 0.8738 (mmm-85) REVERT: A 631 ASP cc_start: 0.7517 (p0) cc_final: 0.7286 (p0) REVERT: A 633 MET cc_start: 0.7989 (mtp) cc_final: 0.7287 (ttm) REVERT: A 635 MET cc_start: 0.9172 (tmm) cc_final: 0.8873 (tmm) REVERT: A 658 LEU cc_start: 0.9787 (mt) cc_final: 0.9356 (mt) REVERT: A 671 GLN cc_start: 0.8777 (mt0) cc_final: 0.8238 (mt0) REVERT: A 675 SER cc_start: 0.9590 (m) cc_final: 0.9292 (p) REVERT: A 691 GLN cc_start: 0.9496 (pt0) cc_final: 0.8640 (pt0) REVERT: A 695 TYR cc_start: 0.9286 (m-80) cc_final: 0.8170 (m-80) REVERT: A 699 CYS cc_start: 0.8445 (p) cc_final: 0.7871 (p) REVERT: A 744 MET cc_start: 0.8926 (mmp) cc_final: 0.8393 (mmm) REVERT: A 754 LYS cc_start: 0.9444 (mmpt) cc_final: 0.9221 (mmmt) REVERT: A 755 ILE cc_start: 0.9553 (mt) cc_final: 0.9142 (mt) REVERT: A 760 TRP cc_start: 0.9272 (m100) cc_final: 0.8403 (m100) REVERT: A 773 ASP cc_start: 0.9255 (m-30) cc_final: 0.9015 (t0) REVERT: A 780 ILE cc_start: 0.9329 (pt) cc_final: 0.8994 (pt) REVERT: A 816 LEU cc_start: 0.9790 (tp) cc_final: 0.9548 (tp) REVERT: A 830 MET cc_start: 0.8962 (mmp) cc_final: 0.7899 (mmp) REVERT: A 907 VAL cc_start: 0.9524 (t) cc_final: 0.9200 (t) REVERT: A 926 GLN cc_start: 0.9020 (mt0) cc_final: 0.8707 (mt0) REVERT: A 928 MET cc_start: 0.9008 (ttm) cc_final: 0.8608 (ttm) REVERT: A 934 LYS cc_start: 0.9542 (tptm) cc_final: 0.9052 (mmmm) REVERT: A 977 MET cc_start: 0.8853 (ttt) cc_final: 0.8627 (tpt) REVERT: A 994 GLU cc_start: 0.9160 (mp0) cc_final: 0.8667 (mp0) REVERT: A 995 TYR cc_start: 0.9543 (t80) cc_final: 0.9247 (t80) REVERT: A 1018 TYR cc_start: 0.8809 (t80) cc_final: 0.8531 (t80) REVERT: A 1056 ASP cc_start: 0.9101 (t0) cc_final: 0.8863 (t0) REVERT: A 1121 ASP cc_start: 0.8312 (p0) cc_final: 0.7514 (p0) REVERT: A 1175 MET cc_start: 0.8937 (tmm) cc_final: 0.8689 (tmm) REVERT: A 1200 MET cc_start: 0.9089 (mmp) cc_final: 0.8732 (mmp) REVERT: A 1306 TYR cc_start: 0.8046 (m-80) cc_final: 0.7723 (m-80) REVERT: A 1331 LYS cc_start: 0.9868 (tttp) cc_final: 0.9645 (tptp) REVERT: A 1545 ASP cc_start: 0.9013 (t70) cc_final: 0.8566 (t0) REVERT: A 1610 PHE cc_start: 0.9458 (m-10) cc_final: 0.9239 (m-80) REVERT: A 1616 GLU cc_start: 0.8773 (pp20) cc_final: 0.8536 (pp20) REVERT: B 25 PHE cc_start: 0.9171 (m-80) cc_final: 0.8753 (m-10) REVERT: B 215 MET cc_start: 0.8237 (mmm) cc_final: 0.7589 (mmm) REVERT: B 271 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8866 (p) REVERT: B 296 ASP cc_start: 0.8900 (m-30) cc_final: 0.7302 (t0) REVERT: B 369 ASP cc_start: 0.9568 (m-30) cc_final: 0.9302 (t70) REVERT: B 373 MET cc_start: 0.9705 (tpt) cc_final: 0.9287 (tpp) REVERT: B 415 GLU cc_start: 0.9230 (tp30) cc_final: 0.8845 (tp30) REVERT: B 416 LYS cc_start: 0.9495 (mmtt) cc_final: 0.8913 (mmmm) REVERT: B 419 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9165 (mt-10) REVERT: B 420 TYR cc_start: 0.9463 (t80) cc_final: 0.9247 (t80) REVERT: B 465 LEU cc_start: 0.9712 (mt) cc_final: 0.9376 (tt) REVERT: B 500 PHE cc_start: 0.9496 (m-80) cc_final: 0.9105 (m-80) REVERT: B 505 ARG cc_start: 0.9006 (tpt90) cc_final: 0.8706 (tpp80) REVERT: B 542 LEU cc_start: 0.9535 (tp) cc_final: 0.9309 (tp) REVERT: B 672 MET cc_start: 0.8819 (mtm) cc_final: 0.8410 (mtp) REVERT: B 703 LEU cc_start: 0.9681 (mm) cc_final: 0.9281 (mm) REVERT: B 716 MET cc_start: 0.9363 (mtm) cc_final: 0.8782 (mtm) REVERT: B 728 THR cc_start: 0.9565 (m) cc_final: 0.9096 (p) REVERT: B 740 LYS cc_start: 0.9553 (pttm) cc_final: 0.9079 (ttpp) REVERT: B 762 MET cc_start: 0.9094 (mmp) cc_final: 0.8743 (mmp) REVERT: B 763 ASP cc_start: 0.8595 (t0) cc_final: 0.8328 (t0) REVERT: B 779 THR cc_start: 0.9108 (p) cc_final: 0.8655 (p) REVERT: B 782 ASP cc_start: 0.9052 (p0) cc_final: 0.8396 (p0) REVERT: B 785 ASP cc_start: 0.6807 (m-30) cc_final: 0.5960 (m-30) REVERT: B 886 ASN cc_start: 0.8959 (m-40) cc_final: 0.8693 (m-40) REVERT: B 915 ASP cc_start: 0.8371 (m-30) cc_final: 0.7705 (m-30) REVERT: B 954 PHE cc_start: 0.9027 (m-10) cc_final: 0.8610 (m-80) REVERT: B 959 THR cc_start: 0.9338 (p) cc_final: 0.8830 (p) REVERT: B 1005 TYR cc_start: 0.8894 (m-10) cc_final: 0.8559 (m-10) REVERT: B 1034 GLN cc_start: 0.9001 (mt0) cc_final: 0.8529 (mp10) REVERT: B 1054 SER cc_start: 0.9393 (p) cc_final: 0.9125 (t) REVERT: B 1074 MET cc_start: 0.8954 (mtt) cc_final: 0.8677 (mmm) REVERT: B 1077 ASP cc_start: 0.9486 (m-30) cc_final: 0.9154 (m-30) REVERT: B 1084 THR cc_start: 0.9072 (p) cc_final: 0.8660 (p) REVERT: B 1133 MET cc_start: 0.9454 (tpt) cc_final: 0.9051 (ppp) REVERT: B 1178 ILE cc_start: 0.9685 (pt) cc_final: 0.9189 (pt) REVERT: B 1180 PHE cc_start: 0.9271 (t80) cc_final: 0.8648 (t80) REVERT: B 1201 GLU cc_start: 0.9072 (tp30) cc_final: 0.8792 (tp30) REVERT: C 56 LEU cc_start: 0.9755 (mp) cc_final: 0.9380 (mp) REVERT: C 63 ILE cc_start: 0.9438 (mp) cc_final: 0.8996 (mp) REVERT: C 67 PHE cc_start: 0.9587 (m-80) cc_final: 0.9298 (m-80) REVERT: C 71 MET cc_start: 0.9614 (mmp) cc_final: 0.9338 (mmm) REVERT: C 82 TYR cc_start: 0.8904 (m-10) cc_final: 0.8638 (m-10) REVERT: C 112 MET cc_start: 0.9144 (mtm) cc_final: 0.8888 (mtp) REVERT: C 192 LEU cc_start: 0.9505 (tp) cc_final: 0.9145 (tt) REVERT: C 229 LEU cc_start: 0.9153 (tp) cc_final: 0.8952 (tp) REVERT: C 272 LYS cc_start: 0.9581 (tptt) cc_final: 0.9277 (tptm) REVERT: C 290 LYS cc_start: 0.9664 (mmpt) cc_final: 0.9420 (mmmt) REVERT: D 94 ARG cc_start: 0.9477 (ptt-90) cc_final: 0.8836 (tmm160) REVERT: E 22 MET cc_start: 0.9063 (ttm) cc_final: 0.8740 (ttp) REVERT: E 50 MET cc_start: 0.8151 (mmm) cc_final: 0.7625 (mpp) REVERT: E 82 PHE cc_start: 0.9358 (m-80) cc_final: 0.8813 (m-80) REVERT: E 112 TYR cc_start: 0.9384 (p90) cc_final: 0.8757 (p90) REVERT: E 168 TYR cc_start: 0.9253 (m-80) cc_final: 0.8858 (m-80) REVERT: E 192 ARG cc_start: 0.9316 (ptp-110) cc_final: 0.8963 (ttp-110) REVERT: E 213 ILE cc_start: 0.8338 (tt) cc_final: 0.7373 (tp) REVERT: F 66 ARG cc_start: 0.9450 (mtp180) cc_final: 0.9238 (mtm110) REVERT: F 103 MET cc_start: 0.9524 (mmt) cc_final: 0.9316 (mmm) REVERT: F 145 ASP cc_start: 0.9101 (m-30) cc_final: 0.8463 (m-30) REVERT: G 53 TYR cc_start: 0.9000 (m-80) cc_final: 0.8748 (m-80) REVERT: G 71 MET cc_start: 0.8454 (mmm) cc_final: 0.7915 (mmm) REVERT: G 84 TYR cc_start: 0.7966 (p90) cc_final: 0.6955 (p90) REVERT: H 42 ILE cc_start: 0.9652 (pt) cc_final: 0.9155 (mp) REVERT: H 95 TYR cc_start: 0.9140 (t80) cc_final: 0.8244 (t80) REVERT: H 97 MET cc_start: 0.8301 (mtm) cc_final: 0.6028 (mtm) REVERT: H 116 TYR cc_start: 0.8561 (m-80) cc_final: 0.8095 (m-80) REVERT: H 141 TYR cc_start: 0.8335 (m-80) cc_final: 0.8009 (m-80) REVERT: I 71 LEU cc_start: 0.9180 (mt) cc_final: 0.8900 (tp) REVERT: I 94 MET cc_start: 0.1156 (mmt) cc_final: 0.0656 (tpp) REVERT: J 9 SER cc_start: 0.9458 (m) cc_final: 0.9222 (p) REVERT: J 14 VAL cc_start: 0.9183 (m) cc_final: 0.8951 (m) REVERT: J 16 ASP cc_start: 0.8851 (p0) cc_final: 0.8426 (p0) REVERT: J 41 LEU cc_start: 0.8739 (mp) cc_final: 0.8170 (mp) REVERT: J 58 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8680 (tp30) REVERT: K 69 ASP cc_start: 0.8529 (p0) cc_final: 0.8190 (p0) REVERT: K 99 ASN cc_start: 0.8923 (p0) cc_final: 0.8406 (p0) REVERT: K 101 LEU cc_start: 0.9109 (tp) cc_final: 0.8893 (tp) REVERT: K 135 PHE cc_start: 0.9345 (t80) cc_final: 0.8425 (t80) REVERT: L 33 GLU cc_start: 0.9625 (tp30) cc_final: 0.9211 (tm-30) REVERT: M 52 VAL cc_start: 0.7970 (t) cc_final: 0.7700 (p) REVERT: N 27 ASP cc_start: 0.9742 (t0) cc_final: 0.9449 (t70) REVERT: N 34 HIS cc_start: 0.8681 (t-90) cc_final: 0.8426 (t70) REVERT: O 125 TRP cc_start: 0.8169 (p-90) cc_final: 0.7090 (p-90) REVERT: O 467 MET cc_start: 0.3066 (mmp) cc_final: 0.2622 (mmt) REVERT: O 505 PHE cc_start: 0.4961 (t80) cc_final: 0.3430 (t80) REVERT: O 508 ARG cc_start: 0.6840 (ptp-170) cc_final: 0.5717 (tmt-80) REVERT: O 525 MET cc_start: -0.1727 (tpt) cc_final: -0.2422 (tpt) outliers start: 4 outliers final: 1 residues processed: 874 average time/residue: 0.2669 time to fit residues: 380.8306 Evaluate side-chains 695 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 693 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 360 optimal weight: 0.7980 chunk 368 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 417 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 398 optimal weight: 9.9990 chunk 516 optimal weight: 40.0000 chunk 313 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN C 99 HIS E 146 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS O 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.112273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076693 restraints weight = 189961.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076836 restraints weight = 149382.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077447 restraints weight = 122886.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078012 restraints weight = 108305.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078706 restraints weight = 98076.064| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.939 44443 Z= 0.393 Angle : 0.693 19.026 60029 Z= 0.364 Chirality : 0.045 0.367 6174 Planarity : 0.005 0.142 7686 Dihedral : 14.429 86.239 7179 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.44 % Favored : 95.36 % Rotamer: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.02 (0.11), residues: 5522 helix: 1.24 (0.11), residues: 2266 sheet: -0.47 (0.18), residues: 762 loop : -1.02 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 241 TYR 0.022 0.002 TYR O 482 PHE 0.035 0.002 PHE N 29 TRP 0.058 0.002 TRP B 143 HIS 0.010 0.002 HIS G 119 Details of bonding type rmsd covalent geometry : bond 0.01144 (44412) covalent geometry : angle 0.68316 (60002) hydrogen bonds : bond 0.04073 ( 2132) hydrogen bonds : angle 5.17093 ( 6059) metal coordination : bond 0.01033 ( 22) metal coordination : angle 5.42369 ( 27) Misc. bond : bond 0.00442 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 871 time to evaluate : 1.396 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9686 (mt) cc_final: 0.9296 (mp) REVERT: A 134 TYR cc_start: 0.9228 (m-80) cc_final: 0.8916 (m-80) REVERT: A 135 LYS cc_start: 0.9625 (ptpp) cc_final: 0.9416 (pttp) REVERT: A 216 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8278 (mmt90) REVERT: A 331 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8959 (mm-30) REVERT: A 472 MET cc_start: 0.8527 (mmp) cc_final: 0.8093 (mmt) REVERT: A 520 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.7938 (mtt-85) REVERT: A 537 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8270 (mp10) REVERT: A 585 ASP cc_start: 0.8960 (m-30) cc_final: 0.8723 (m-30) REVERT: A 613 THR cc_start: 0.9574 (p) cc_final: 0.9074 (t) REVERT: A 614 LEU cc_start: 0.9237 (mt) cc_final: 0.9022 (mt) REVERT: A 635 MET cc_start: 0.9334 (tmm) cc_final: 0.8884 (tmm) REVERT: A 658 LEU cc_start: 0.9764 (mt) cc_final: 0.9350 (mt) REVERT: A 675 SER cc_start: 0.9608 (m) cc_final: 0.9323 (p) REVERT: A 686 PHE cc_start: 0.8816 (m-10) cc_final: 0.7371 (m-10) REVERT: A 691 GLN cc_start: 0.9482 (pt0) cc_final: 0.8557 (pt0) REVERT: A 695 TYR cc_start: 0.9312 (m-80) cc_final: 0.8164 (m-80) REVERT: A 699 CYS cc_start: 0.8413 (p) cc_final: 0.7804 (p) REVERT: A 754 LYS cc_start: 0.9490 (mmpt) cc_final: 0.9285 (mmmt) REVERT: A 755 ILE cc_start: 0.9484 (mt) cc_final: 0.9143 (mt) REVERT: A 760 TRP cc_start: 0.9276 (m100) cc_final: 0.8477 (m100) REVERT: A 773 ASP cc_start: 0.9271 (m-30) cc_final: 0.9058 (t0) REVERT: A 776 LEU cc_start: 0.9413 (tp) cc_final: 0.9187 (tp) REVERT: A 780 ILE cc_start: 0.9373 (pt) cc_final: 0.9050 (pt) REVERT: A 816 LEU cc_start: 0.9790 (tp) cc_final: 0.9566 (tp) REVERT: A 830 MET cc_start: 0.9114 (mmp) cc_final: 0.8238 (mmm) REVERT: A 925 MET cc_start: 0.9232 (mmm) cc_final: 0.8923 (mmm) REVERT: A 926 GLN cc_start: 0.8955 (mt0) cc_final: 0.8604 (mt0) REVERT: A 928 MET cc_start: 0.8936 (ttm) cc_final: 0.8550 (ttm) REVERT: A 994 GLU cc_start: 0.9212 (mp0) cc_final: 0.8986 (mp0) REVERT: A 995 TYR cc_start: 0.9547 (t80) cc_final: 0.9182 (t80) REVERT: A 1056 ASP cc_start: 0.9097 (t0) cc_final: 0.8889 (t0) REVERT: A 1068 PHE cc_start: 0.9467 (t80) cc_final: 0.9194 (t80) REVERT: A 1085 LEU cc_start: 0.8930 (tp) cc_final: 0.8425 (mt) REVERT: A 1121 ASP cc_start: 0.8206 (p0) cc_final: 0.7411 (p0) REVERT: A 1200 MET cc_start: 0.9231 (mmp) cc_final: 0.8893 (mmp) REVERT: A 1479 ASP cc_start: 0.9412 (m-30) cc_final: 0.9057 (t0) REVERT: A 1545 ASP cc_start: 0.8910 (t70) cc_final: 0.8419 (t0) REVERT: A 1568 ASN cc_start: 0.9236 (m110) cc_final: 0.9035 (m110) REVERT: A 1610 PHE cc_start: 0.9382 (m-10) cc_final: 0.9140 (m-10) REVERT: A 1616 GLU cc_start: 0.8793 (pp20) cc_final: 0.8477 (pp20) REVERT: A 1621 PHE cc_start: 0.9266 (m-80) cc_final: 0.9031 (m-80) REVERT: A 1647 ASN cc_start: 0.8935 (t0) cc_final: 0.8436 (t0) REVERT: B 25 PHE cc_start: 0.9031 (m-10) cc_final: 0.8639 (m-10) REVERT: B 137 LEU cc_start: 0.9512 (tp) cc_final: 0.9097 (tp) REVERT: B 143 TRP cc_start: 0.7713 (m-10) cc_final: 0.7354 (m-10) REVERT: B 215 MET cc_start: 0.8359 (mmm) cc_final: 0.6536 (mmm) REVERT: B 249 VAL cc_start: 0.9063 (t) cc_final: 0.8825 (t) REVERT: B 261 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8241 (tmm-80) REVERT: B 262 PHE cc_start: 0.9374 (p90) cc_final: 0.9103 (p90) REVERT: B 296 ASP cc_start: 0.8887 (m-30) cc_final: 0.7361 (t0) REVERT: B 373 MET cc_start: 0.9767 (tpt) cc_final: 0.9444 (tpp) REVERT: B 392 ASP cc_start: 0.8173 (m-30) cc_final: 0.7239 (m-30) REVERT: B 415 GLU cc_start: 0.9209 (tp30) cc_final: 0.8416 (tp30) REVERT: B 416 LYS cc_start: 0.9544 (mmtt) cc_final: 0.9011 (mmtp) REVERT: B 419 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9044 (mt-10) REVERT: B 420 TYR cc_start: 0.9291 (t80) cc_final: 0.8939 (t80) REVERT: B 465 LEU cc_start: 0.9669 (mt) cc_final: 0.9320 (tt) REVERT: B 489 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 500 PHE cc_start: 0.9495 (m-80) cc_final: 0.9039 (m-80) REVERT: B 504 HIS cc_start: 0.8706 (t70) cc_final: 0.8488 (t70) REVERT: B 505 ARG cc_start: 0.9054 (tpt90) cc_final: 0.8730 (tpp80) REVERT: B 672 MET cc_start: 0.8761 (mtm) cc_final: 0.8470 (ptp) REVERT: B 703 LEU cc_start: 0.9626 (mm) cc_final: 0.9299 (mm) REVERT: B 715 ASN cc_start: 0.9026 (m-40) cc_final: 0.8250 (m110) REVERT: B 723 LYS cc_start: 0.9606 (mtmt) cc_final: 0.9358 (mtmt) REVERT: B 728 THR cc_start: 0.9591 (m) cc_final: 0.9209 (p) REVERT: B 740 LYS cc_start: 0.9542 (pttm) cc_final: 0.9177 (ptmt) REVERT: B 762 MET cc_start: 0.9180 (mmp) cc_final: 0.8933 (mmp) REVERT: B 763 ASP cc_start: 0.8551 (t0) cc_final: 0.8124 (t0) REVERT: B 782 ASP cc_start: 0.8965 (p0) cc_final: 0.8363 (p0) REVERT: B 785 ASP cc_start: 0.6666 (m-30) cc_final: 0.5575 (m-30) REVERT: B 787 MET cc_start: 0.8658 (ppp) cc_final: 0.8458 (ppp) REVERT: B 886 ASN cc_start: 0.9028 (m-40) cc_final: 0.8738 (m-40) REVERT: B 904 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9131 (ttmm) REVERT: B 915 ASP cc_start: 0.8140 (m-30) cc_final: 0.7585 (m-30) REVERT: B 917 PHE cc_start: 0.8687 (m-80) cc_final: 0.8429 (m-10) REVERT: B 924 LYS cc_start: 0.8991 (tttm) cc_final: 0.8454 (tmtt) REVERT: B 935 ASP cc_start: 0.9644 (m-30) cc_final: 0.9392 (m-30) REVERT: B 936 MET cc_start: 0.9051 (mmm) cc_final: 0.8717 (mmm) REVERT: B 954 PHE cc_start: 0.9173 (m-10) cc_final: 0.8496 (m-80) REVERT: B 958 MET cc_start: 0.9553 (ptp) cc_final: 0.9133 (pmm) REVERT: B 959 THR cc_start: 0.9402 (p) cc_final: 0.8695 (p) REVERT: B 1013 MET cc_start: 0.9251 (tpt) cc_final: 0.8843 (tmm) REVERT: B 1034 GLN cc_start: 0.8973 (mt0) cc_final: 0.8519 (mp10) REVERT: B 1039 MET cc_start: 0.4331 (tmm) cc_final: 0.4004 (tmm) REVERT: B 1074 MET cc_start: 0.8880 (mtt) cc_final: 0.8594 (mmm) REVERT: B 1077 ASP cc_start: 0.9510 (m-30) cc_final: 0.9252 (m-30) REVERT: B 1084 THR cc_start: 0.9157 (p) cc_final: 0.8925 (p) REVERT: B 1133 MET cc_start: 0.9406 (tpt) cc_final: 0.9019 (ppp) REVERT: B 1180 PHE cc_start: 0.9301 (t80) cc_final: 0.8756 (t80) REVERT: C 54 PHE cc_start: 0.9470 (p90) cc_final: 0.9258 (p90) REVERT: C 56 LEU cc_start: 0.9774 (mp) cc_final: 0.9328 (mp) REVERT: C 71 MET cc_start: 0.9584 (mmp) cc_final: 0.8964 (mmm) REVERT: C 112 MET cc_start: 0.9227 (mtm) cc_final: 0.8922 (mtp) REVERT: C 272 LYS cc_start: 0.9645 (tptt) cc_final: 0.9295 (tptm) REVERT: C 290 LYS cc_start: 0.9666 (mmpt) cc_final: 0.9437 (mmmt) REVERT: C 308 MET cc_start: 0.7834 (mmm) cc_final: 0.7517 (mmm) REVERT: D 20 VAL cc_start: 0.7319 (t) cc_final: 0.7085 (t) REVERT: D 29 GLN cc_start: 0.9120 (mp10) cc_final: 0.8851 (mp10) REVERT: E 1 MET cc_start: 0.9156 (tmm) cc_final: 0.8900 (tmm) REVERT: E 21 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8989 (mt-10) REVERT: E 22 MET cc_start: 0.9202 (ttm) cc_final: 0.8841 (ttp) REVERT: E 50 MET cc_start: 0.8355 (mmm) cc_final: 0.7821 (mpp) REVERT: E 58 MET cc_start: 0.9071 (mpp) cc_final: 0.8427 (mpp) REVERT: E 82 PHE cc_start: 0.9358 (m-80) cc_final: 0.8755 (m-80) REVERT: E 112 TYR cc_start: 0.9336 (p90) cc_final: 0.8771 (p90) REVERT: E 168 TYR cc_start: 0.9160 (m-80) cc_final: 0.8762 (m-80) REVERT: E 192 ARG cc_start: 0.9275 (ptp-110) cc_final: 0.9008 (mtm110) REVERT: E 213 ILE cc_start: 0.8419 (tt) cc_final: 0.7611 (tp) REVERT: F 66 ARG cc_start: 0.9477 (mtp180) cc_final: 0.9251 (mtm110) REVERT: F 84 TYR cc_start: 0.8361 (m-10) cc_final: 0.8119 (m-10) REVERT: F 137 TYR cc_start: 0.8843 (m-80) cc_final: 0.8451 (m-10) REVERT: F 145 ASP cc_start: 0.9128 (m-30) cc_final: 0.8376 (m-30) REVERT: F 151 LEU cc_start: 0.8722 (mm) cc_final: 0.8477 (mm) REVERT: G 52 MET cc_start: 0.9395 (mmm) cc_final: 0.9186 (mmm) REVERT: G 53 TYR cc_start: 0.9005 (m-80) cc_final: 0.8755 (m-80) REVERT: G 71 MET cc_start: 0.8439 (mmm) cc_final: 0.7768 (mmp) REVERT: H 22 LYS cc_start: 0.8982 (mttt) cc_final: 0.7810 (mtpt) REVERT: H 42 ILE cc_start: 0.9589 (pt) cc_final: 0.9112 (mp) REVERT: H 95 TYR cc_start: 0.9099 (t80) cc_final: 0.8188 (t80) REVERT: H 97 MET cc_start: 0.8297 (mtm) cc_final: 0.6602 (mtm) REVERT: H 116 TYR cc_start: 0.8471 (m-80) cc_final: 0.8251 (m-80) REVERT: H 141 TYR cc_start: 0.8175 (m-80) cc_final: 0.7968 (m-80) REVERT: I 56 PHE cc_start: 0.9000 (m-80) cc_final: 0.8493 (m-80) REVERT: J 41 LEU cc_start: 0.8694 (mp) cc_final: 0.8238 (mp) REVERT: J 58 GLU cc_start: 0.9494 (mm-30) cc_final: 0.8672 (tp30) REVERT: K 69 ASP cc_start: 0.8433 (p0) cc_final: 0.8022 (p0) REVERT: K 99 ASN cc_start: 0.9046 (p0) cc_final: 0.8570 (p0) REVERT: K 100 LEU cc_start: 0.9256 (mt) cc_final: 0.8694 (tt) REVERT: K 135 PHE cc_start: 0.9384 (t80) cc_final: 0.8647 (t80) REVERT: M 52 VAL cc_start: 0.7940 (t) cc_final: 0.7640 (p) REVERT: M 100 VAL cc_start: 0.8444 (t) cc_final: 0.7438 (t) REVERT: N 27 ASP cc_start: 0.9752 (t0) cc_final: 0.9437 (t70) REVERT: N 34 HIS cc_start: 0.8791 (t-90) cc_final: 0.8575 (t70) REVERT: O 467 MET cc_start: 0.3031 (mmp) cc_final: 0.2792 (mmt) REVERT: O 505 PHE cc_start: 0.5032 (t80) cc_final: 0.3511 (t80) REVERT: O 508 ARG cc_start: 0.6925 (ptp-170) cc_final: 0.5786 (tpt90) REVERT: O 525 MET cc_start: -0.1541 (tpt) cc_final: -0.2198 (tpt) REVERT: O 527 MET cc_start: 0.5365 (tpt) cc_final: 0.5121 (tmm) outliers start: 1 outliers final: 0 residues processed: 872 average time/residue: 0.2196 time to fit residues: 311.2917 Evaluate side-chains 702 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 143 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 464 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 532 optimal weight: 8.9990 chunk 484 optimal weight: 6.9990 chunk 359 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS N 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.110068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076208 restraints weight = 195890.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075408 restraints weight = 150311.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076189 restraints weight = 123249.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076898 restraints weight = 104692.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077420 restraints weight = 93099.832| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.936 44443 Z= 0.403 Angle : 0.722 18.787 60029 Z= 0.378 Chirality : 0.046 0.364 6174 Planarity : 0.006 0.270 7686 Dihedral : 14.428 145.567 7179 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.23 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.06 (0.11), residues: 5522 helix: 1.23 (0.11), residues: 2261 sheet: -0.53 (0.19), residues: 759 loop : -1.06 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 91 TYR 0.025 0.002 TYR O 482 PHE 0.036 0.002 PHE O 189 TRP 0.063 0.003 TRP G 166 HIS 0.009 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.01158 (44412) covalent geometry : angle 0.71169 (60002) hydrogen bonds : bond 0.04236 ( 2132) hydrogen bonds : angle 5.21611 ( 6059) metal coordination : bond 0.01102 ( 22) metal coordination : angle 5.87552 ( 27) Misc. bond : bond 0.00607 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 851 time to evaluate : 1.618 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9604 (mt) cc_final: 0.9265 (mp) REVERT: A 134 TYR cc_start: 0.9253 (m-80) cc_final: 0.9050 (m-80) REVERT: A 251 ILE cc_start: 0.9227 (mt) cc_final: 0.8907 (tp) REVERT: A 331 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8971 (mm-30) REVERT: A 339 PHE cc_start: 0.9491 (m-80) cc_final: 0.9277 (m-80) REVERT: A 472 MET cc_start: 0.8532 (mmp) cc_final: 0.8092 (mmp) REVERT: A 520 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.7952 (mtt-85) REVERT: A 578 TYR cc_start: 0.9462 (m-10) cc_final: 0.8898 (m-80) REVERT: A 608 LEU cc_start: 0.9455 (mt) cc_final: 0.9246 (mt) REVERT: A 631 ASP cc_start: 0.8552 (p0) cc_final: 0.8237 (p0) REVERT: A 633 MET cc_start: 0.9060 (mmt) cc_final: 0.8824 (mmt) REVERT: A 635 MET cc_start: 0.9326 (tmm) cc_final: 0.8826 (tmm) REVERT: A 650 LEU cc_start: 0.9107 (mt) cc_final: 0.8864 (mt) REVERT: A 658 LEU cc_start: 0.9776 (mt) cc_final: 0.9359 (mt) REVERT: A 671 GLN cc_start: 0.8711 (mt0) cc_final: 0.8251 (mt0) REVERT: A 675 SER cc_start: 0.9590 (m) cc_final: 0.9321 (p) REVERT: A 686 PHE cc_start: 0.8973 (m-10) cc_final: 0.8287 (m-10) REVERT: A 691 GLN cc_start: 0.9493 (pt0) cc_final: 0.8542 (pt0) REVERT: A 695 TYR cc_start: 0.9354 (m-80) cc_final: 0.8305 (m-80) REVERT: A 699 CYS cc_start: 0.8472 (p) cc_final: 0.7843 (p) REVERT: A 744 MET cc_start: 0.8849 (mmp) cc_final: 0.8548 (mmm) REVERT: A 780 ILE cc_start: 0.9394 (pt) cc_final: 0.9106 (pt) REVERT: A 816 LEU cc_start: 0.9754 (tp) cc_final: 0.9443 (tp) REVERT: A 830 MET cc_start: 0.9205 (mmp) cc_final: 0.8387 (mmm) REVERT: A 925 MET cc_start: 0.9352 (mmm) cc_final: 0.9095 (mmm) REVERT: A 926 GLN cc_start: 0.9051 (mt0) cc_final: 0.8843 (mt0) REVERT: A 928 MET cc_start: 0.8977 (ttm) cc_final: 0.8621 (ttm) REVERT: A 934 LYS cc_start: 0.9487 (tptm) cc_final: 0.9187 (mmmm) REVERT: A 944 MET cc_start: 0.8948 (mmm) cc_final: 0.8730 (mmm) REVERT: A 995 TYR cc_start: 0.9530 (t80) cc_final: 0.9217 (t80) REVERT: A 1018 TYR cc_start: 0.8537 (t80) cc_final: 0.8304 (t80) REVERT: A 1056 ASP cc_start: 0.9091 (t0) cc_final: 0.8864 (t0) REVERT: A 1121 ASP cc_start: 0.8165 (p0) cc_final: 0.7365 (p0) REVERT: A 1170 MET cc_start: 0.9509 (mmt) cc_final: 0.9145 (mmt) REVERT: A 1175 MET cc_start: 0.8977 (tmm) cc_final: 0.8765 (tmm) REVERT: A 1200 MET cc_start: 0.9329 (mmp) cc_final: 0.9045 (mmp) REVERT: A 1471 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8675 (tp30) REVERT: A 1479 ASP cc_start: 0.9345 (m-30) cc_final: 0.9113 (t0) REVERT: A 1545 ASP cc_start: 0.8922 (t70) cc_final: 0.8376 (t0) REVERT: A 1568 ASN cc_start: 0.9235 (m110) cc_final: 0.8995 (m110) REVERT: A 1589 MET cc_start: 0.9559 (ttt) cc_final: 0.9284 (tmm) REVERT: A 1594 THR cc_start: 0.9635 (p) cc_final: 0.9358 (p) REVERT: A 1610 PHE cc_start: 0.9411 (m-10) cc_final: 0.9147 (m-10) REVERT: A 1616 GLU cc_start: 0.8733 (pp20) cc_final: 0.8408 (pp20) REVERT: A 1655 ASP cc_start: 0.9016 (t0) cc_final: 0.8422 (t0) REVERT: A 1656 VAL cc_start: 0.9605 (t) cc_final: 0.9318 (t) REVERT: B 25 PHE cc_start: 0.9027 (m-10) cc_final: 0.8459 (m-10) REVERT: B 143 TRP cc_start: 0.8024 (m-10) cc_final: 0.7418 (m-10) REVERT: B 158 CYS cc_start: 0.8289 (m) cc_final: 0.8050 (m) REVERT: B 204 ARG cc_start: 0.9232 (ptp-110) cc_final: 0.8655 (mtm-85) REVERT: B 215 MET cc_start: 0.8366 (mmm) cc_final: 0.7887 (mmm) REVERT: B 373 MET cc_start: 0.9787 (tpt) cc_final: 0.9454 (tpp) REVERT: B 376 PHE cc_start: 0.9160 (t80) cc_final: 0.8912 (t80) REVERT: B 395 ASP cc_start: 0.9483 (t70) cc_final: 0.9263 (t0) REVERT: B 415 GLU cc_start: 0.9020 (tp30) cc_final: 0.8580 (tp30) REVERT: B 416 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9029 (mttp) REVERT: B 419 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9075 (mt-10) REVERT: B 420 TYR cc_start: 0.9267 (t80) cc_final: 0.9042 (t80) REVERT: B 465 LEU cc_start: 0.9703 (mt) cc_final: 0.9370 (tt) REVERT: B 489 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 500 PHE cc_start: 0.9508 (m-80) cc_final: 0.9067 (m-80) REVERT: B 504 HIS cc_start: 0.8784 (t70) cc_final: 0.8542 (t70) REVERT: B 505 ARG cc_start: 0.9009 (tpt90) cc_final: 0.8486 (tpt-90) REVERT: B 528 LEU cc_start: 0.9709 (mp) cc_final: 0.9390 (mp) REVERT: B 625 GLU cc_start: 0.8930 (tt0) cc_final: 0.8205 (mm-30) REVERT: B 672 MET cc_start: 0.8810 (mtm) cc_final: 0.8506 (ptp) REVERT: B 703 LEU cc_start: 0.9631 (mm) cc_final: 0.9268 (mm) REVERT: B 716 MET cc_start: 0.9354 (mtm) cc_final: 0.8778 (mtm) REVERT: B 717 TYR cc_start: 0.9231 (t80) cc_final: 0.8819 (t80) REVERT: B 723 LYS cc_start: 0.9616 (mtmt) cc_final: 0.9315 (mtmt) REVERT: B 728 THR cc_start: 0.9590 (m) cc_final: 0.9327 (p) REVERT: B 742 TYR cc_start: 0.9011 (m-10) cc_final: 0.8414 (m-10) REVERT: B 762 MET cc_start: 0.9227 (mmp) cc_final: 0.8979 (mmp) REVERT: B 763 ASP cc_start: 0.8592 (t0) cc_final: 0.8130 (t0) REVERT: B 781 TYR cc_start: 0.7152 (m-80) cc_final: 0.6810 (m-80) REVERT: B 782 ASP cc_start: 0.9013 (p0) cc_final: 0.8511 (p0) REVERT: B 785 ASP cc_start: 0.6285 (m-30) cc_final: 0.5032 (m-30) REVERT: B 917 PHE cc_start: 0.8604 (m-80) cc_final: 0.8357 (m-10) REVERT: B 924 LYS cc_start: 0.9029 (tttm) cc_final: 0.8458 (tmtt) REVERT: B 929 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7043 (ttm110) REVERT: B 931 TRP cc_start: 0.9171 (t-100) cc_final: 0.8506 (t-100) REVERT: B 935 ASP cc_start: 0.9669 (m-30) cc_final: 0.8990 (t0) REVERT: B 936 MET cc_start: 0.9353 (mmm) cc_final: 0.9112 (mmm) REVERT: B 946 ASP cc_start: 0.9034 (m-30) cc_final: 0.8731 (m-30) REVERT: B 954 PHE cc_start: 0.9111 (m-10) cc_final: 0.8393 (m-80) REVERT: B 958 MET cc_start: 0.9495 (ptp) cc_final: 0.9104 (pmm) REVERT: B 959 THR cc_start: 0.9416 (p) cc_final: 0.8660 (p) REVERT: B 1025 ASP cc_start: 0.9243 (m-30) cc_final: 0.9035 (m-30) REVERT: B 1034 GLN cc_start: 0.8964 (mt0) cc_final: 0.8576 (mp10) REVERT: B 1039 MET cc_start: 0.4273 (tmm) cc_final: 0.4071 (tmm) REVERT: B 1074 MET cc_start: 0.8983 (mtt) cc_final: 0.8690 (mmm) REVERT: B 1077 ASP cc_start: 0.9497 (m-30) cc_final: 0.9236 (m-30) REVERT: B 1084 THR cc_start: 0.9143 (p) cc_final: 0.8879 (p) REVERT: B 1133 MET cc_start: 0.9424 (tpt) cc_final: 0.9035 (ppp) REVERT: B 1180 PHE cc_start: 0.9282 (t80) cc_final: 0.8549 (t80) REVERT: C 63 ILE cc_start: 0.9578 (mp) cc_final: 0.8981 (mp) REVERT: C 67 PHE cc_start: 0.9631 (m-80) cc_final: 0.9362 (m-80) REVERT: C 71 MET cc_start: 0.9531 (mmp) cc_final: 0.8986 (mmm) REVERT: C 112 MET cc_start: 0.9320 (mtm) cc_final: 0.9083 (mtp) REVERT: C 167 LEU cc_start: 0.9110 (mt) cc_final: 0.8902 (mt) REVERT: C 207 HIS cc_start: 0.9063 (m-70) cc_final: 0.8837 (m90) REVERT: C 272 LYS cc_start: 0.9593 (tptt) cc_final: 0.9272 (tptm) REVERT: D 29 GLN cc_start: 0.9093 (mp10) cc_final: 0.8813 (mp10) REVERT: D 94 ARG cc_start: 0.9564 (ptt-90) cc_final: 0.9011 (ttp80) REVERT: E 1 MET cc_start: 0.9195 (tmm) cc_final: 0.8989 (tmm) REVERT: E 18 THR cc_start: 0.9140 (m) cc_final: 0.8869 (p) REVERT: E 21 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9175 (mt-10) REVERT: E 22 MET cc_start: 0.9231 (ttm) cc_final: 0.8850 (ttp) REVERT: E 50 MET cc_start: 0.8404 (mmm) cc_final: 0.8007 (mpp) REVERT: E 58 MET cc_start: 0.9078 (mpp) cc_final: 0.8876 (mpp) REVERT: E 82 PHE cc_start: 0.9381 (m-80) cc_final: 0.8798 (m-80) REVERT: E 112 TYR cc_start: 0.9339 (p90) cc_final: 0.8854 (p90) REVERT: E 168 TYR cc_start: 0.9200 (m-80) cc_final: 0.8757 (m-10) REVERT: E 192 ARG cc_start: 0.9335 (ptp-110) cc_final: 0.8950 (mtm110) REVERT: E 213 ILE cc_start: 0.8557 (tt) cc_final: 0.7701 (tp) REVERT: F 66 ARG cc_start: 0.9502 (mtp180) cc_final: 0.9277 (mtm110) REVERT: F 90 ARG cc_start: 0.9523 (mmm-85) cc_final: 0.9320 (mmm-85) REVERT: F 99 LEU cc_start: 0.9536 (tp) cc_final: 0.9295 (tp) REVERT: F 103 MET cc_start: 0.9470 (mmp) cc_final: 0.9226 (mmm) REVERT: F 135 ARG cc_start: 0.9069 (tpt90) cc_final: 0.8783 (tpt-90) REVERT: F 145 ASP cc_start: 0.9186 (m-30) cc_final: 0.8826 (m-30) REVERT: G 40 ARG cc_start: 0.9600 (tpt90) cc_final: 0.9306 (tpt90) REVERT: G 46 TYR cc_start: 0.8828 (t80) cc_final: 0.8550 (t80) REVERT: G 48 SER cc_start: 0.7273 (p) cc_final: 0.6609 (p) REVERT: G 53 TYR cc_start: 0.9007 (m-80) cc_final: 0.8775 (m-80) REVERT: G 71 MET cc_start: 0.8451 (mmm) cc_final: 0.7724 (mmp) REVERT: G 125 TRP cc_start: 0.9162 (t-100) cc_final: 0.8720 (t-100) REVERT: H 22 LYS cc_start: 0.9101 (mttt) cc_final: 0.8730 (mtpt) REVERT: H 95 TYR cc_start: 0.9092 (t80) cc_final: 0.8653 (t80) REVERT: H 116 TYR cc_start: 0.8592 (m-80) cc_final: 0.8361 (m-80) REVERT: H 141 TYR cc_start: 0.8211 (m-80) cc_final: 0.7931 (m-80) REVERT: I 94 MET cc_start: 0.0947 (mmt) cc_final: 0.0415 (tpp) REVERT: J 41 LEU cc_start: 0.8804 (mp) cc_final: 0.8368 (mp) REVERT: J 49 MET cc_start: 0.9495 (mmm) cc_final: 0.9069 (mmm) REVERT: J 58 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8319 (tm-30) REVERT: K 69 ASP cc_start: 0.8495 (p0) cc_final: 0.7939 (p0) REVERT: K 99 ASN cc_start: 0.9080 (p0) cc_final: 0.8623 (p0) REVERT: K 100 LEU cc_start: 0.9334 (mt) cc_final: 0.8903 (mt) REVERT: K 101 LEU cc_start: 0.9167 (tp) cc_final: 0.8861 (tp) REVERT: K 135 PHE cc_start: 0.9259 (t80) cc_final: 0.8621 (t80) REVERT: L 28 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7926 (mmpt) REVERT: M 52 VAL cc_start: 0.7972 (t) cc_final: 0.7710 (p) REVERT: N 27 ASP cc_start: 0.9781 (t0) cc_final: 0.9456 (t70) REVERT: N 133 PHE cc_start: 0.8090 (m-80) cc_final: 0.7638 (m-80) REVERT: N 169 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8719 (mt-10) REVERT: O 525 MET cc_start: -0.0823 (tpt) cc_final: -0.1631 (tpt) REVERT: O 527 MET cc_start: 0.5464 (tpt) cc_final: 0.5167 (tmm) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.2214 time to fit residues: 307.4710 Evaluate side-chains 684 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 325 optimal weight: 5.9990 chunk 510 optimal weight: 50.0000 chunk 112 optimal weight: 7.9990 chunk 473 optimal weight: 30.0000 chunk 454 optimal weight: 40.0000 chunk 286 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 chunk 471 optimal weight: 50.0000 chunk 377 optimal weight: 0.7980 chunk 411 optimal weight: 0.9980 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1180 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN K 106 GLN ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 546 ASN ** O 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.110780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075969 restraints weight = 192765.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075548 restraints weight = 150004.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.076255 restraints weight = 124054.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.076718 restraints weight = 107391.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077374 restraints weight = 99818.735| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.8308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.936 44443 Z= 0.386 Angle : 0.698 20.610 60029 Z= 0.365 Chirality : 0.045 0.348 6174 Planarity : 0.007 0.426 7686 Dihedral : 14.444 176.685 7179 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.93 % Favored : 94.88 % Rotamer: Outliers : 0.02 % Allowed : 1.34 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.01 (0.11), residues: 5522 helix: 1.30 (0.11), residues: 2266 sheet: -0.57 (0.18), residues: 774 loop : -1.02 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 156 TYR 0.072 0.002 TYR E 211 PHE 0.034 0.002 PHE B 895 TRP 0.062 0.003 TRP G 166 HIS 0.010 0.002 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.01137 (44412) covalent geometry : angle 0.68987 (60002) hydrogen bonds : bond 0.03975 ( 2132) hydrogen bonds : angle 5.14078 ( 6059) metal coordination : bond 0.00929 ( 22) metal coordination : angle 5.18754 ( 27) Misc. bond : bond 0.00486 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 844 time to evaluate : 1.154 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: 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: 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: 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: 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: 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: A 130 ILE cc_start: 0.9572 (mt) cc_final: 0.9062 (mm) REVERT: A 205 ARG cc_start: 0.9148 (tpm170) cc_final: 0.8931 (tpm170) REVERT: A 251 ILE cc_start: 0.9212 (mt) cc_final: 0.8909 (tp) REVERT: A 331 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8999 (mm-30) REVERT: A 339 PHE cc_start: 0.9532 (m-80) cc_final: 0.9328 (m-80) REVERT: A 472 MET cc_start: 0.8498 (mmp) cc_final: 0.8066 (mmt) REVERT: A 520 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8032 (mtt-85) REVERT: A 578 TYR cc_start: 0.9456 (m-10) cc_final: 0.8875 (m-80) REVERT: A 595 LEU cc_start: 0.9724 (mt) cc_final: 0.9444 (mt) REVERT: A 601 MET cc_start: 0.8526 (mmm) cc_final: 0.8187 (mmm) REVERT: A 608 LEU cc_start: 0.9486 (mt) cc_final: 0.9278 (mt) REVERT: A 633 MET cc_start: 0.8895 (mmt) cc_final: 0.8413 (mmm) REVERT: A 635 MET cc_start: 0.9349 (tmm) cc_final: 0.8880 (tmm) REVERT: A 650 LEU cc_start: 0.9112 (mt) cc_final: 0.8779 (mt) REVERT: A 658 LEU cc_start: 0.9754 (mt) cc_final: 0.9349 (mt) REVERT: A 671 GLN cc_start: 0.8769 (mt0) cc_final: 0.8189 (mt0) REVERT: A 675 SER cc_start: 0.9551 (m) cc_final: 0.9256 (p) REVERT: A 686 PHE cc_start: 0.9046 (m-10) cc_final: 0.7891 (m-10) REVERT: A 691 GLN cc_start: 0.9500 (pt0) cc_final: 0.8565 (pt0) REVERT: A 695 TYR cc_start: 0.9380 (m-80) cc_final: 0.8423 (m-80) REVERT: A 699 CYS cc_start: 0.8618 (p) cc_final: 0.8127 (p) REVERT: A 744 MET cc_start: 0.8779 (mmp) cc_final: 0.8404 (mmm) REVERT: A 780 ILE cc_start: 0.9354 (pt) cc_final: 0.9108 (pt) REVERT: A 816 LEU cc_start: 0.9777 (tp) cc_final: 0.9482 (tp) REVERT: A 830 MET cc_start: 0.9222 (mmp) cc_final: 0.8438 (mmm) REVERT: A 925 MET cc_start: 0.9323 (mmm) cc_final: 0.9065 (mmm) REVERT: A 926 GLN cc_start: 0.9121 (mt0) cc_final: 0.8910 (mt0) REVERT: A 928 MET cc_start: 0.9006 (ttm) cc_final: 0.8663 (ttm) REVERT: A 934 LYS cc_start: 0.9439 (tptm) cc_final: 0.8974 (mmmm) REVERT: A 995 TYR cc_start: 0.9609 (t80) cc_final: 0.9253 (t80) REVERT: A 1004 GLU cc_start: 0.9228 (pt0) cc_final: 0.9014 (pt0) REVERT: A 1006 LEU cc_start: 0.9785 (mt) cc_final: 0.9536 (mt) REVERT: A 1018 TYR cc_start: 0.8548 (t80) cc_final: 0.8286 (t80) REVERT: A 1056 ASP cc_start: 0.9056 (t0) cc_final: 0.8848 (t0) REVERT: A 1121 ASP cc_start: 0.8181 (p0) cc_final: 0.7421 (p0) REVERT: A 1175 MET cc_start: 0.8988 (tmm) cc_final: 0.8779 (tmm) REVERT: A 1195 GLU cc_start: 0.9653 (tm-30) cc_final: 0.9099 (tp30) REVERT: A 1200 MET cc_start: 0.9291 (mmp) cc_final: 0.9083 (mmp) REVERT: A 1471 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8674 (tp30) REVERT: A 1479 ASP cc_start: 0.9382 (m-30) cc_final: 0.9174 (t0) REVERT: A 1545 ASP cc_start: 0.8902 (t70) cc_final: 0.8414 (t0) REVERT: A 1568 ASN cc_start: 0.9294 (m110) cc_final: 0.9063 (m110) REVERT: A 1610 PHE cc_start: 0.9438 (m-10) cc_final: 0.9238 (m-10) REVERT: A 1616 GLU cc_start: 0.8957 (pp20) cc_final: 0.8565 (pp20) REVERT: A 1621 PHE cc_start: 0.9237 (m-80) cc_final: 0.9010 (m-80) REVERT: A 1647 ASN cc_start: 0.8833 (t0) cc_final: 0.8310 (t0) REVERT: A 1655 ASP cc_start: 0.8745 (t0) cc_final: 0.8158 (t0) REVERT: B 25 PHE cc_start: 0.9109 (m-10) cc_final: 0.8758 (m-10) REVERT: B 143 TRP cc_start: 0.8095 (m-10) cc_final: 0.7541 (m-10) REVERT: B 158 CYS cc_start: 0.8073 (m) cc_final: 0.7857 (m) REVERT: B 204 ARG cc_start: 0.9273 (ptp-110) cc_final: 0.8615 (mtm-85) REVERT: B 215 MET cc_start: 0.8304 (mmm) cc_final: 0.7808 (mmm) REVERT: B 289 PHE cc_start: 0.9611 (t80) cc_final: 0.9332 (t80) REVERT: B 373 MET cc_start: 0.9764 (tpt) cc_final: 0.9368 (tpp) REVERT: B 395 ASP cc_start: 0.9490 (t70) cc_final: 0.9272 (t0) REVERT: B 411 MET cc_start: 0.9216 (mmm) cc_final: 0.8756 (mmm) REVERT: B 415 GLU cc_start: 0.9058 (tp30) cc_final: 0.8589 (tp30) REVERT: B 416 LYS cc_start: 0.9434 (mmtt) cc_final: 0.8884 (mmtp) REVERT: B 419 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8829 (mt-10) REVERT: B 465 LEU cc_start: 0.9709 (mt) cc_final: 0.9356 (tt) REVERT: B 489 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 500 PHE cc_start: 0.9511 (m-80) cc_final: 0.9066 (m-80) REVERT: B 504 HIS cc_start: 0.8778 (t70) cc_final: 0.8498 (t70) REVERT: B 505 ARG cc_start: 0.9011 (tpt90) cc_final: 0.8591 (tpt-90) REVERT: B 591 LYS cc_start: 0.9480 (tptp) cc_final: 0.9118 (tptt) REVERT: B 625 GLU cc_start: 0.8972 (tt0) cc_final: 0.8301 (mm-30) REVERT: B 672 MET cc_start: 0.8759 (mtm) cc_final: 0.8420 (ptp) REVERT: B 703 LEU cc_start: 0.9642 (mm) cc_final: 0.9252 (mm) REVERT: B 715 ASN cc_start: 0.9134 (m-40) cc_final: 0.8454 (m110) REVERT: B 716 MET cc_start: 0.9369 (mtm) cc_final: 0.8807 (mtm) REVERT: B 717 TYR cc_start: 0.9237 (t80) cc_final: 0.8762 (t80) REVERT: B 728 THR cc_start: 0.9516 (m) cc_final: 0.9281 (p) REVERT: B 740 LYS cc_start: 0.9513 (pttm) cc_final: 0.9032 (ttpp) REVERT: B 763 ASP cc_start: 0.8579 (t0) cc_final: 0.8262 (t0) REVERT: B 781 TYR cc_start: 0.7254 (m-80) cc_final: 0.6777 (m-80) REVERT: B 782 ASP cc_start: 0.8956 (p0) cc_final: 0.8413 (p0) REVERT: B 785 ASP cc_start: 0.6334 (m-30) cc_final: 0.5523 (m-30) REVERT: B 917 PHE cc_start: 0.8591 (m-80) cc_final: 0.8348 (m-10) REVERT: B 936 MET cc_start: 0.9367 (mmm) cc_final: 0.8973 (mmm) REVERT: B 946 ASP cc_start: 0.8951 (m-30) cc_final: 0.8724 (m-30) REVERT: B 954 PHE cc_start: 0.9163 (m-10) cc_final: 0.8407 (m-80) REVERT: B 958 MET cc_start: 0.9554 (ptp) cc_final: 0.9155 (pmm) REVERT: B 959 THR cc_start: 0.9461 (p) cc_final: 0.8893 (p) REVERT: B 1005 TYR cc_start: 0.9046 (m-10) cc_final: 0.8760 (m-10) REVERT: B 1034 GLN cc_start: 0.8989 (mt0) cc_final: 0.8579 (mp10) REVERT: B 1039 MET cc_start: 0.4294 (tmm) cc_final: 0.4013 (tmm) REVERT: B 1074 MET cc_start: 0.8913 (mtt) cc_final: 0.8649 (mmm) REVERT: B 1077 ASP cc_start: 0.9488 (m-30) cc_final: 0.9220 (m-30) REVERT: B 1084 THR cc_start: 0.9183 (p) cc_final: 0.8965 (p) REVERT: B 1133 MET cc_start: 0.9428 (tpt) cc_final: 0.8979 (ppp) REVERT: B 1180 PHE cc_start: 0.9368 (t80) cc_final: 0.8590 (t80) REVERT: B 1201 GLU cc_start: 0.9386 (tp30) cc_final: 0.8706 (tp30) REVERT: C 54 PHE cc_start: 0.9516 (p90) cc_final: 0.9315 (p90) REVERT: C 56 LEU cc_start: 0.9769 (mp) cc_final: 0.9538 (mp) REVERT: C 63 ILE cc_start: 0.9573 (mp) cc_final: 0.8908 (mp) REVERT: C 67 PHE cc_start: 0.9636 (m-80) cc_final: 0.9366 (m-80) REVERT: C 71 MET cc_start: 0.9576 (mmp) cc_final: 0.8977 (mmm) REVERT: C 112 MET cc_start: 0.9347 (mtm) cc_final: 0.9100 (mtp) REVERT: C 167 LEU cc_start: 0.9188 (mt) cc_final: 0.8976 (mt) REVERT: C 193 LEU cc_start: 0.9563 (mt) cc_final: 0.9329 (mt) REVERT: C 229 LEU cc_start: 0.8997 (tp) cc_final: 0.8784 (tp) REVERT: D 20 VAL cc_start: 0.7495 (t) cc_final: 0.7181 (t) REVERT: D 29 GLN cc_start: 0.9113 (mp10) cc_final: 0.8884 (mp10) REVERT: D 94 ARG cc_start: 0.9527 (ptt-90) cc_final: 0.8727 (ttp80) REVERT: D 99 LEU cc_start: 0.7387 (tp) cc_final: 0.6974 (tp) REVERT: E 21 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9124 (mt-10) REVERT: E 22 MET cc_start: 0.9324 (ttm) cc_final: 0.8965 (ttp) REVERT: E 50 MET cc_start: 0.8447 (mmm) cc_final: 0.8055 (mpp) REVERT: E 82 PHE cc_start: 0.9422 (m-80) cc_final: 0.8855 (m-80) REVERT: E 112 TYR cc_start: 0.9289 (p90) cc_final: 0.8826 (p90) REVERT: E 168 TYR cc_start: 0.9262 (m-80) cc_final: 0.9032 (m-10) REVERT: E 179 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7925 (mm-40) REVERT: E 213 ILE cc_start: 0.8575 (tt) cc_final: 0.7666 (tp) REVERT: F 66 ARG cc_start: 0.9543 (mtp180) cc_final: 0.9294 (mtm110) REVERT: F 67 LYS cc_start: 0.9524 (ptpp) cc_final: 0.9321 (pttp) REVERT: F 84 TYR cc_start: 0.8510 (m-10) cc_final: 0.8251 (m-10) REVERT: F 89 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9390 (mm-30) REVERT: F 90 ARG cc_start: 0.9506 (mmm-85) cc_final: 0.9213 (mmm-85) REVERT: F 100 GLN cc_start: 0.9322 (mp10) cc_final: 0.8901 (mm-40) REVERT: F 137 TYR cc_start: 0.9006 (m-80) cc_final: 0.8159 (t80) REVERT: F 151 LEU cc_start: 0.8488 (mm) cc_final: 0.8201 (mm) REVERT: G 48 SER cc_start: 0.7439 (p) cc_final: 0.6666 (p) REVERT: G 51 PRO cc_start: 0.8320 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: G 52 MET cc_start: 0.9120 (mmp) cc_final: 0.8905 (mmm) REVERT: G 71 MET cc_start: 0.8591 (mmm) cc_final: 0.8202 (mmm) REVERT: G 125 TRP cc_start: 0.9234 (t-100) cc_final: 0.8919 (t-100) REVERT: H 42 ILE cc_start: 0.9543 (tt) cc_final: 0.9217 (mp) REVERT: H 95 TYR cc_start: 0.8992 (t80) cc_final: 0.8206 (t80) REVERT: H 116 TYR cc_start: 0.8545 (m-80) cc_final: 0.8326 (m-80) REVERT: H 141 TYR cc_start: 0.8199 (m-80) cc_final: 0.7948 (m-80) REVERT: J 16 ASP cc_start: 0.9021 (p0) cc_final: 0.8699 (p0) REVERT: J 39 LEU cc_start: 0.9476 (mm) cc_final: 0.9253 (mm) REVERT: J 41 LEU cc_start: 0.8808 (mp) cc_final: 0.8592 (mp) REVERT: J 49 MET cc_start: 0.9487 (mmm) cc_final: 0.9036 (mmm) REVERT: J 58 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8307 (tp30) REVERT: K 69 ASP cc_start: 0.8544 (p0) cc_final: 0.8041 (p0) REVERT: K 99 ASN cc_start: 0.9108 (p0) cc_final: 0.8638 (p0) REVERT: K 100 LEU cc_start: 0.9306 (mt) cc_final: 0.8934 (mt) REVERT: K 101 LEU cc_start: 0.9164 (tp) cc_final: 0.8868 (tp) REVERT: K 135 PHE cc_start: 0.9266 (t80) cc_final: 0.8639 (t80) REVERT: M 51 PHE cc_start: 0.8055 (m-80) cc_final: 0.7752 (m-10) REVERT: M 52 VAL cc_start: 0.7993 (t) cc_final: 0.7608 (p) REVERT: N 27 ASP cc_start: 0.9775 (t0) cc_final: 0.9444 (t70) REVERT: N 169 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8760 (mt-10) REVERT: O 467 MET cc_start: 0.3536 (mmp) cc_final: 0.3309 (mmp) REVERT: O 525 MET cc_start: -0.0632 (tpt) cc_final: -0.1297 (tpt) REVERT: O 527 MET cc_start: 0.5561 (tpt) cc_final: 0.5317 (tmm) outliers start: 1 outliers final: 0 residues processed: 845 average time/residue: 0.2376 time to fit residues: 327.1798 Evaluate side-chains 673 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 468 optimal weight: 10.0000 chunk 491 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 506 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 437 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 467 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 590 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1320 GLN A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN N 34 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.111459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076384 restraints weight = 189926.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076112 restraints weight = 144859.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076778 restraints weight = 119601.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077545 restraints weight = 103530.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078010 restraints weight = 92389.049| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.8519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.932 44443 Z= 0.371 Angle : 0.687 19.635 60029 Z= 0.358 Chirality : 0.046 0.357 6174 Planarity : 0.006 0.300 7686 Dihedral : 14.233 166.455 7179 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.78 % Favored : 95.00 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.06 (0.11), residues: 5522 helix: 1.39 (0.11), residues: 2260 sheet: -0.61 (0.18), residues: 754 loop : -0.99 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 156 TYR 0.033 0.002 TYR A 134 PHE 0.038 0.002 PHE B 440 TRP 0.062 0.002 TRP G 166 HIS 0.012 0.001 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.01113 (44412) covalent geometry : angle 0.68021 (60002) hydrogen bonds : bond 0.03860 ( 2132) hydrogen bonds : angle 5.00651 ( 6059) metal coordination : bond 0.00738 ( 22) metal coordination : angle 4.48959 ( 27) Misc. bond : bond 0.00827 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 854 time to evaluate : 1.679 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: 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: 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: 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: 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: 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: A 130 ILE cc_start: 0.9497 (mt) cc_final: 0.9272 (mp) REVERT: A 134 TYR cc_start: 0.8783 (m-80) cc_final: 0.8532 (m-80) REVERT: A 251 ILE cc_start: 0.9181 (mt) cc_final: 0.8901 (tp) REVERT: A 331 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9001 (mm-30) REVERT: A 461 GLU cc_start: 0.8824 (pp20) cc_final: 0.8523 (tp30) REVERT: A 472 MET cc_start: 0.8670 (mmp) cc_final: 0.8185 (mmt) REVERT: A 520 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8117 (mtt-85) REVERT: A 578 TYR cc_start: 0.9474 (m-10) cc_final: 0.8894 (m-80) REVERT: A 595 LEU cc_start: 0.9731 (mt) cc_final: 0.9185 (mp) REVERT: A 627 ASP cc_start: 0.8348 (p0) cc_final: 0.8086 (p0) REVERT: A 633 MET cc_start: 0.9051 (mmt) cc_final: 0.8785 (mmp) REVERT: A 635 MET cc_start: 0.9354 (tmm) cc_final: 0.8872 (tmm) REVERT: A 650 LEU cc_start: 0.9086 (mt) cc_final: 0.8784 (mt) REVERT: A 658 LEU cc_start: 0.9748 (mt) cc_final: 0.9259 (mt) REVERT: A 671 GLN cc_start: 0.8724 (mt0) cc_final: 0.8111 (mt0) REVERT: A 675 SER cc_start: 0.9523 (m) cc_final: 0.9227 (p) REVERT: A 686 PHE cc_start: 0.9121 (m-10) cc_final: 0.8768 (m-10) REVERT: A 691 GLN cc_start: 0.9501 (pt0) cc_final: 0.8668 (pt0) REVERT: A 695 TYR cc_start: 0.9364 (m-80) cc_final: 0.8388 (m-80) REVERT: A 699 CYS cc_start: 0.8568 (p) cc_final: 0.8125 (p) REVERT: A 744 MET cc_start: 0.8761 (mmp) cc_final: 0.8458 (mmm) REVERT: A 780 ILE cc_start: 0.9260 (pt) cc_final: 0.9009 (pt) REVERT: A 816 LEU cc_start: 0.9763 (tp) cc_final: 0.9492 (tp) REVERT: A 830 MET cc_start: 0.9271 (mmp) cc_final: 0.8438 (mmp) REVERT: A 925 MET cc_start: 0.9320 (mmm) cc_final: 0.9051 (mmm) REVERT: A 926 GLN cc_start: 0.9177 (mt0) cc_final: 0.8926 (mt0) REVERT: A 928 MET cc_start: 0.9013 (ttm) cc_final: 0.8710 (ttm) REVERT: A 934 LYS cc_start: 0.9448 (tptm) cc_final: 0.9114 (mmmm) REVERT: A 944 MET cc_start: 0.8995 (mmm) cc_final: 0.8766 (mmm) REVERT: A 995 TYR cc_start: 0.9623 (t80) cc_final: 0.9178 (t80) REVERT: A 1006 LEU cc_start: 0.9777 (mt) cc_final: 0.9487 (mt) REVERT: A 1018 TYR cc_start: 0.8580 (t80) cc_final: 0.8341 (t80) REVERT: A 1068 PHE cc_start: 0.9477 (t80) cc_final: 0.9238 (t80) REVERT: A 1195 GLU cc_start: 0.9651 (tm-30) cc_final: 0.8911 (tp30) REVERT: A 1471 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8636 (tp30) REVERT: A 1545 ASP cc_start: 0.8843 (t70) cc_final: 0.8290 (t0) REVERT: A 1568 ASN cc_start: 0.9282 (m110) cc_final: 0.9047 (m110) REVERT: A 1583 ASP cc_start: 0.9440 (m-30) cc_final: 0.9133 (m-30) REVERT: A 1610 PHE cc_start: 0.9409 (m-10) cc_final: 0.9207 (m-10) REVERT: A 1616 GLU cc_start: 0.8880 (pp20) cc_final: 0.8540 (pp20) REVERT: A 1647 ASN cc_start: 0.8828 (t0) cc_final: 0.8224 (t0) REVERT: B 25 PHE cc_start: 0.9198 (m-10) cc_final: 0.8766 (m-10) REVERT: B 143 TRP cc_start: 0.8006 (m-10) cc_final: 0.7440 (m-10) REVERT: B 157 ASP cc_start: 0.8877 (t0) cc_final: 0.8660 (p0) REVERT: B 158 CYS cc_start: 0.8243 (m) cc_final: 0.7395 (m) REVERT: B 179 GLU cc_start: 0.9393 (mp0) cc_final: 0.9123 (mp0) REVERT: B 204 ARG cc_start: 0.9312 (ptp-110) cc_final: 0.8587 (mtm-85) REVERT: B 215 MET cc_start: 0.8311 (mmm) cc_final: 0.8006 (mmm) REVERT: B 289 PHE cc_start: 0.9552 (t80) cc_final: 0.9282 (t80) REVERT: B 373 MET cc_start: 0.9735 (tpt) cc_final: 0.9274 (tpp) REVERT: B 377 MET cc_start: 0.8589 (mmm) cc_final: 0.7964 (mmm) REVERT: B 395 ASP cc_start: 0.9565 (t70) cc_final: 0.9326 (t70) REVERT: B 411 MET cc_start: 0.9199 (mmm) cc_final: 0.8731 (mmm) REVERT: B 415 GLU cc_start: 0.9013 (tp30) cc_final: 0.8710 (tp30) REVERT: B 416 LYS cc_start: 0.9412 (mmtt) cc_final: 0.8888 (mmtp) REVERT: B 420 TYR cc_start: 0.9200 (t80) cc_final: 0.8715 (t80) REVERT: B 465 LEU cc_start: 0.9722 (mt) cc_final: 0.9375 (tt) REVERT: B 489 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 500 PHE cc_start: 0.9486 (m-80) cc_final: 0.9040 (m-80) REVERT: B 504 HIS cc_start: 0.8744 (t70) cc_final: 0.8455 (t70) REVERT: B 505 ARG cc_start: 0.9014 (tpt90) cc_final: 0.8560 (tpt-90) REVERT: B 521 LEU cc_start: 0.9495 (mp) cc_final: 0.9246 (mp) REVERT: B 576 THR cc_start: 0.8156 (m) cc_final: 0.7774 (p) REVERT: B 672 MET cc_start: 0.8742 (mtm) cc_final: 0.8396 (ptp) REVERT: B 715 ASN cc_start: 0.9119 (m-40) cc_final: 0.8402 (m110) REVERT: B 716 MET cc_start: 0.9333 (mtm) cc_final: 0.8823 (mtm) REVERT: B 717 TYR cc_start: 0.9346 (t80) cc_final: 0.8643 (t80) REVERT: B 723 LYS cc_start: 0.9609 (mtmt) cc_final: 0.9394 (mtmm) REVERT: B 740 LYS cc_start: 0.9517 (pttm) cc_final: 0.9009 (ttpp) REVERT: B 763 ASP cc_start: 0.8602 (t0) cc_final: 0.8306 (t0) REVERT: B 778 TYR cc_start: 0.8082 (t80) cc_final: 0.7729 (t80) REVERT: B 782 ASP cc_start: 0.8871 (p0) cc_final: 0.8401 (p0) REVERT: B 785 ASP cc_start: 0.6492 (m-30) cc_final: 0.5878 (m-30) REVERT: B 917 PHE cc_start: 0.8478 (m-80) cc_final: 0.8277 (m-10) REVERT: B 936 MET cc_start: 0.9430 (mmm) cc_final: 0.9026 (mmm) REVERT: B 946 ASP cc_start: 0.8996 (m-30) cc_final: 0.8758 (m-30) REVERT: B 954 PHE cc_start: 0.9140 (m-10) cc_final: 0.8397 (m-80) REVERT: B 958 MET cc_start: 0.9541 (ptp) cc_final: 0.9186 (pmm) REVERT: B 959 THR cc_start: 0.9520 (p) cc_final: 0.8811 (p) REVERT: B 1013 MET cc_start: 0.8650 (tpp) cc_final: 0.8256 (tpp) REVERT: B 1022 LEU cc_start: 0.9694 (mt) cc_final: 0.9344 (mt) REVERT: B 1025 ASP cc_start: 0.9336 (m-30) cc_final: 0.9128 (m-30) REVERT: B 1034 GLN cc_start: 0.8920 (mt0) cc_final: 0.8525 (mp10) REVERT: B 1039 MET cc_start: 0.4645 (tmm) cc_final: 0.4293 (tmm) REVERT: B 1084 THR cc_start: 0.9156 (p) cc_final: 0.8931 (p) REVERT: B 1133 MET cc_start: 0.9405 (tpt) cc_final: 0.8930 (ppp) REVERT: B 1180 PHE cc_start: 0.9363 (t80) cc_final: 0.8700 (t80) REVERT: B 1201 GLU cc_start: 0.9018 (tp30) cc_final: 0.8738 (tp30) REVERT: C 56 LEU cc_start: 0.9765 (mp) cc_final: 0.9516 (mp) REVERT: C 71 MET cc_start: 0.9534 (mmp) cc_final: 0.8850 (mmm) REVERT: C 82 TYR cc_start: 0.8906 (m-10) cc_final: 0.8534 (m-10) REVERT: C 167 LEU cc_start: 0.9167 (mt) cc_final: 0.8967 (mt) REVERT: C 193 LEU cc_start: 0.9585 (mt) cc_final: 0.9374 (mt) REVERT: C 229 LEU cc_start: 0.9086 (tp) cc_final: 0.8882 (tp) REVERT: C 308 MET cc_start: 0.7060 (tpt) cc_final: 0.6110 (mmm) REVERT: D 29 GLN cc_start: 0.9100 (mp10) cc_final: 0.8891 (mp10) REVERT: D 94 ARG cc_start: 0.9508 (ptt-90) cc_final: 0.8597 (ttp80) REVERT: D 99 LEU cc_start: 0.7624 (tp) cc_final: 0.7215 (tp) REVERT: E 21 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9175 (mt-10) REVERT: E 22 MET cc_start: 0.9373 (ttm) cc_final: 0.9014 (ttp) REVERT: E 50 MET cc_start: 0.8452 (mmm) cc_final: 0.8150 (mpp) REVERT: E 58 MET cc_start: 0.9235 (mpp) cc_final: 0.8480 (mpp) REVERT: E 82 PHE cc_start: 0.9425 (m-80) cc_final: 0.8847 (m-80) REVERT: E 112 TYR cc_start: 0.9283 (p90) cc_final: 0.8809 (p90) REVERT: E 164 LEU cc_start: 0.9445 (tp) cc_final: 0.9192 (tp) REVERT: E 168 TYR cc_start: 0.9184 (m-80) cc_final: 0.8834 (m-10) REVERT: E 179 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7817 (mm-40) REVERT: E 213 ILE cc_start: 0.8609 (tt) cc_final: 0.7757 (tp) REVERT: F 66 ARG cc_start: 0.9551 (mtp180) cc_final: 0.9300 (mtm110) REVERT: F 67 LYS cc_start: 0.9471 (ptpp) cc_final: 0.9261 (pttp) REVERT: F 87 LYS cc_start: 0.9516 (mmpt) cc_final: 0.9298 (mmmt) REVERT: F 89 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9390 (mm-30) REVERT: F 90 ARG cc_start: 0.9484 (mmm-85) cc_final: 0.9072 (mmm-85) REVERT: F 100 GLN cc_start: 0.9316 (mp10) cc_final: 0.8890 (mm-40) REVERT: F 137 TYR cc_start: 0.8858 (m-80) cc_final: 0.8201 (t80) REVERT: F 151 LEU cc_start: 0.8440 (mm) cc_final: 0.8154 (mm) REVERT: G 40 ARG cc_start: 0.9593 (tpt90) cc_final: 0.9368 (tpt90) REVERT: G 51 PRO cc_start: 0.8391 (Cg_exo) cc_final: 0.8150 (Cg_endo) REVERT: G 71 MET cc_start: 0.8677 (mmm) cc_final: 0.8219 (mmp) REVERT: G 125 TRP cc_start: 0.9333 (t-100) cc_final: 0.8973 (t-100) REVERT: H 22 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8454 (mtmt) REVERT: H 42 ILE cc_start: 0.9397 (tt) cc_final: 0.9000 (mp) REVERT: H 95 TYR cc_start: 0.8981 (t80) cc_final: 0.8296 (t80) REVERT: H 116 TYR cc_start: 0.8572 (m-80) cc_final: 0.8344 (m-80) REVERT: H 121 LEU cc_start: 0.9291 (mm) cc_final: 0.8943 (mt) REVERT: H 141 TYR cc_start: 0.8253 (m-80) cc_final: 0.8024 (m-80) REVERT: I 56 PHE cc_start: 0.8845 (m-80) cc_final: 0.8143 (m-80) REVERT: I 94 MET cc_start: 0.1305 (mmt) cc_final: 0.0662 (tpp) REVERT: J 41 LEU cc_start: 0.8722 (mp) cc_final: 0.8262 (mp) REVERT: J 49 MET cc_start: 0.9526 (mmm) cc_final: 0.9030 (mmm) REVERT: J 58 GLU cc_start: 0.9444 (mm-30) cc_final: 0.8390 (tp30) REVERT: K 69 ASP cc_start: 0.8595 (p0) cc_final: 0.8158 (p0) REVERT: K 99 ASN cc_start: 0.9049 (p0) cc_final: 0.8524 (p0) REVERT: K 100 LEU cc_start: 0.9293 (mt) cc_final: 0.8559 (tt) REVERT: K 124 LEU cc_start: 0.9585 (mm) cc_final: 0.9378 (mm) REVERT: K 125 MET cc_start: 0.9246 (ptp) cc_final: 0.9000 (ptp) REVERT: K 135 PHE cc_start: 0.9258 (t80) cc_final: 0.8596 (t80) REVERT: L 28 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8065 (mmpt) REVERT: M 51 PHE cc_start: 0.8151 (m-80) cc_final: 0.7887 (m-10) REVERT: M 52 VAL cc_start: 0.8046 (t) cc_final: 0.7698 (p) REVERT: M 62 TYR cc_start: 0.9233 (m-80) cc_final: 0.8746 (m-80) REVERT: M 100 VAL cc_start: 0.8163 (t) cc_final: 0.7893 (t) REVERT: N 27 ASP cc_start: 0.9626 (t0) cc_final: 0.9276 (t70) REVERT: O 396 MET cc_start: 0.6371 (mmm) cc_final: 0.6055 (mmm) REVERT: O 467 MET cc_start: 0.3640 (mmp) cc_final: 0.3328 (mmp) REVERT: O 525 MET cc_start: -0.0596 (tpt) cc_final: -0.1144 (tpt) REVERT: O 527 MET cc_start: 0.5778 (tpt) cc_final: 0.5520 (tmm) outliers start: 1 outliers final: 0 residues processed: 855 average time/residue: 0.2662 time to fit residues: 371.8319 Evaluate side-chains 694 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 171 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 420 optimal weight: 40.0000 chunk 460 optimal weight: 8.9990 chunk 514 optimal weight: 40.0000 chunk 140 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 376 optimal weight: 0.5980 chunk 481 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.108123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074212 restraints weight = 202444.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.073480 restraints weight = 157969.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073975 restraints weight = 131118.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074694 restraints weight = 116414.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075251 restraints weight = 104210.114| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.937 44443 Z= 0.411 Angle : 0.752 20.339 60029 Z= 0.394 Chirality : 0.047 0.389 6174 Planarity : 0.007 0.314 7686 Dihedral : 14.246 159.715 7179 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.42 % Rotamer: Outliers : 0.02 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.09 (0.11), residues: 5522 helix: 1.26 (0.11), residues: 2262 sheet: -0.72 (0.18), residues: 754 loop : -1.05 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 444 TYR 0.037 0.002 TYR B 781 PHE 0.046 0.003 PHE B 440 TRP 0.064 0.003 TRP G 166 HIS 0.019 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.01170 (44412) covalent geometry : angle 0.74290 (60002) hydrogen bonds : bond 0.04292 ( 2132) hydrogen bonds : angle 5.23177 ( 6059) metal coordination : bond 0.01257 ( 22) metal coordination : angle 5.55680 ( 27) Misc. bond : bond 0.00701 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 791 time to evaluate : 1.654 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: 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: 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: 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: 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: A 94 LEU cc_start: 0.9534 (tp) cc_final: 0.9232 (tp) REVERT: A 130 ILE cc_start: 0.9520 (mt) cc_final: 0.9281 (mp) REVERT: A 134 TYR cc_start: 0.8922 (m-80) cc_final: 0.8626 (m-80) REVERT: A 251 ILE cc_start: 0.9253 (mt) cc_final: 0.8893 (tp) REVERT: A 331 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9048 (mm-30) REVERT: A 339 PHE cc_start: 0.9657 (m-80) cc_final: 0.9450 (m-80) REVERT: A 472 MET cc_start: 0.8546 (mmp) cc_final: 0.7747 (mmt) REVERT: A 520 ARG cc_start: 0.8839 (mtp-110) cc_final: 0.8132 (mtt-85) REVERT: A 537 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8718 (tp-100) REVERT: A 578 TYR cc_start: 0.9452 (m-10) cc_final: 0.8924 (m-80) REVERT: A 601 MET cc_start: 0.8537 (mmm) cc_final: 0.8208 (mmm) REVERT: A 627 ASP cc_start: 0.8013 (p0) cc_final: 0.7730 (p0) REVERT: A 635 MET cc_start: 0.9325 (tmm) cc_final: 0.8850 (tmm) REVERT: A 650 LEU cc_start: 0.9093 (mt) cc_final: 0.8810 (mt) REVERT: A 658 LEU cc_start: 0.9773 (mt) cc_final: 0.9382 (mt) REVERT: A 671 GLN cc_start: 0.8894 (mt0) cc_final: 0.7958 (mt0) REVERT: A 675 SER cc_start: 0.9558 (m) cc_final: 0.9267 (p) REVERT: A 686 PHE cc_start: 0.9209 (m-10) cc_final: 0.8734 (m-10) REVERT: A 691 GLN cc_start: 0.9509 (pt0) cc_final: 0.8606 (pt0) REVERT: A 695 TYR cc_start: 0.9365 (m-80) cc_final: 0.8436 (m-80) REVERT: A 699 CYS cc_start: 0.8664 (p) cc_final: 0.8304 (p) REVERT: A 744 MET cc_start: 0.8934 (mmp) cc_final: 0.8536 (mmm) REVERT: A 780 ILE cc_start: 0.9328 (pt) cc_final: 0.9111 (pt) REVERT: A 816 LEU cc_start: 0.9774 (tp) cc_final: 0.9493 (tp) REVERT: A 830 MET cc_start: 0.9274 (mmp) cc_final: 0.8421 (mmp) REVERT: A 852 ASP cc_start: 0.9247 (p0) cc_final: 0.8865 (t0) REVERT: A 925 MET cc_start: 0.9366 (mmm) cc_final: 0.9158 (mmm) REVERT: A 926 GLN cc_start: 0.9240 (mt0) cc_final: 0.9022 (mt0) REVERT: A 928 MET cc_start: 0.9211 (ttm) cc_final: 0.8936 (ttm) REVERT: A 934 LYS cc_start: 0.9475 (tptm) cc_final: 0.8893 (mmmm) REVERT: A 950 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8781 (mp10) REVERT: A 1004 GLU cc_start: 0.9307 (pt0) cc_final: 0.9073 (pt0) REVERT: A 1018 TYR cc_start: 0.8667 (t80) cc_final: 0.8444 (t80) REVERT: A 1056 ASP cc_start: 0.9077 (t0) cc_final: 0.8872 (t0) REVERT: A 1200 MET cc_start: 0.9492 (mmp) cc_final: 0.9046 (mmp) REVERT: A 1471 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8733 (tp30) REVERT: A 1545 ASP cc_start: 0.8881 (t70) cc_final: 0.8376 (t0) REVERT: A 1568 ASN cc_start: 0.9308 (m110) cc_final: 0.9061 (m110) REVERT: A 1583 ASP cc_start: 0.9433 (m-30) cc_final: 0.9166 (m-30) REVERT: A 1610 PHE cc_start: 0.9435 (m-10) cc_final: 0.9157 (m-10) REVERT: A 1616 GLU cc_start: 0.9155 (pp20) cc_final: 0.8902 (pp20) REVERT: A 1655 ASP cc_start: 0.9210 (t0) cc_final: 0.8487 (t0) REVERT: B 25 PHE cc_start: 0.9150 (m-10) cc_final: 0.8502 (m-10) REVERT: B 143 TRP cc_start: 0.8060 (m-10) cc_final: 0.7031 (m-10) REVERT: B 157 ASP cc_start: 0.8841 (t0) cc_final: 0.8612 (p0) REVERT: B 204 ARG cc_start: 0.9341 (ptp-110) cc_final: 0.8625 (mtm-85) REVERT: B 215 MET cc_start: 0.8345 (mmm) cc_final: 0.7502 (mmm) REVERT: B 232 TYR cc_start: 0.9088 (m-80) cc_final: 0.8629 (m-10) REVERT: B 261 ARG cc_start: 0.8975 (ttm-80) cc_final: 0.8768 (ttm-80) REVERT: B 373 MET cc_start: 0.9731 (tpt) cc_final: 0.9301 (tpp) REVERT: B 392 ASP cc_start: 0.8374 (m-30) cc_final: 0.8024 (m-30) REVERT: B 411 MET cc_start: 0.9173 (mmm) cc_final: 0.8695 (mmm) REVERT: B 415 GLU cc_start: 0.9194 (tp30) cc_final: 0.8202 (tp30) REVERT: B 416 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9109 (mmtp) REVERT: B 419 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8937 (mp0) REVERT: B 420 TYR cc_start: 0.9173 (t80) cc_final: 0.8663 (t80) REVERT: B 460 LYS cc_start: 0.9770 (mttt) cc_final: 0.9380 (mttt) REVERT: B 465 LEU cc_start: 0.9732 (mt) cc_final: 0.9382 (tt) REVERT: B 489 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 500 PHE cc_start: 0.9462 (m-80) cc_final: 0.9017 (m-80) REVERT: B 504 HIS cc_start: 0.8777 (t70) cc_final: 0.8487 (t70) REVERT: B 523 GLU cc_start: 0.9059 (pm20) cc_final: 0.8363 (pm20) REVERT: B 542 LEU cc_start: 0.9530 (tp) cc_final: 0.9316 (tp) REVERT: B 576 THR cc_start: 0.8041 (m) cc_final: 0.7709 (p) REVERT: B 625 GLU cc_start: 0.8796 (tt0) cc_final: 0.8206 (mm-30) REVERT: B 672 MET cc_start: 0.8800 (mtm) cc_final: 0.8492 (ptp) REVERT: B 717 TYR cc_start: 0.9359 (t80) cc_final: 0.8766 (t80) REVERT: B 740 LYS cc_start: 0.9497 (pttm) cc_final: 0.9035 (ttpp) REVERT: B 763 ASP cc_start: 0.8594 (t0) cc_final: 0.8129 (t0) REVERT: B 782 ASP cc_start: 0.8865 (p0) cc_final: 0.8460 (p0) REVERT: B 785 ASP cc_start: 0.6865 (m-30) cc_final: 0.6110 (m-30) REVERT: B 935 ASP cc_start: 0.9696 (m-30) cc_final: 0.9384 (m-30) REVERT: B 936 MET cc_start: 0.9344 (mmm) cc_final: 0.8899 (mmm) REVERT: B 954 PHE cc_start: 0.9143 (m-10) cc_final: 0.8402 (m-80) REVERT: B 958 MET cc_start: 0.9565 (ptp) cc_final: 0.9202 (pmm) REVERT: B 959 THR cc_start: 0.9395 (p) cc_final: 0.8790 (p) REVERT: B 1005 TYR cc_start: 0.9173 (m-10) cc_final: 0.8445 (m-10) REVERT: B 1013 MET cc_start: 0.8759 (tpp) cc_final: 0.8437 (tpp) REVERT: B 1034 GLN cc_start: 0.8979 (mt0) cc_final: 0.8398 (mp10) REVERT: B 1039 MET cc_start: 0.4883 (tmm) cc_final: 0.4520 (tmm) REVERT: B 1084 THR cc_start: 0.9178 (p) cc_final: 0.8959 (p) REVERT: B 1133 MET cc_start: 0.9488 (tpt) cc_final: 0.9036 (ppp) REVERT: B 1180 PHE cc_start: 0.9411 (t80) cc_final: 0.8862 (t80) REVERT: B 1201 GLU cc_start: 0.9066 (tp30) cc_final: 0.8841 (tp30) REVERT: C 54 PHE cc_start: 0.9503 (p90) cc_final: 0.9251 (p90) REVERT: C 56 LEU cc_start: 0.9783 (mp) cc_final: 0.9557 (mp) REVERT: C 71 MET cc_start: 0.9526 (mmp) cc_final: 0.8853 (mmm) REVERT: C 167 LEU cc_start: 0.9144 (mt) cc_final: 0.8941 (mt) REVERT: C 308 MET cc_start: 0.7224 (tpt) cc_final: 0.6509 (mmm) REVERT: D 29 GLN cc_start: 0.9119 (mp10) cc_final: 0.8914 (mp10) REVERT: D 94 ARG cc_start: 0.9540 (ptt-90) cc_final: 0.8748 (ttp80) REVERT: D 99 LEU cc_start: 0.7912 (tp) cc_final: 0.7550 (tp) REVERT: E 21 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9180 (mt-10) REVERT: E 22 MET cc_start: 0.9332 (ttm) cc_final: 0.8935 (ttp) REVERT: E 50 MET cc_start: 0.8686 (mmm) cc_final: 0.8252 (mpp) REVERT: E 58 MET cc_start: 0.9265 (mpp) cc_final: 0.8568 (mpp) REVERT: E 82 PHE cc_start: 0.9463 (m-80) cc_final: 0.8947 (m-80) REVERT: E 112 TYR cc_start: 0.9316 (p90) cc_final: 0.8939 (p90) REVERT: E 168 TYR cc_start: 0.9200 (m-80) cc_final: 0.8835 (m-10) REVERT: E 179 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7776 (mm-40) REVERT: E 213 ILE cc_start: 0.8839 (tt) cc_final: 0.8058 (tp) REVERT: F 66 ARG cc_start: 0.9578 (mtp180) cc_final: 0.9298 (mtm110) REVERT: F 90 ARG cc_start: 0.9490 (mmm-85) cc_final: 0.9091 (mmm-85) REVERT: F 100 GLN cc_start: 0.9370 (mp10) cc_final: 0.8975 (mm-40) REVERT: F 137 TYR cc_start: 0.8924 (m-80) cc_final: 0.8217 (t80) REVERT: F 151 LEU cc_start: 0.8533 (mm) cc_final: 0.8282 (mm) REVERT: G 51 PRO cc_start: 0.8237 (Cg_exo) cc_final: 0.7979 (Cg_endo) REVERT: G 71 MET cc_start: 0.8899 (mmm) cc_final: 0.8647 (mmm) REVERT: G 125 TRP cc_start: 0.9402 (t-100) cc_final: 0.9010 (t-100) REVERT: H 22 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8620 (mtpt) REVERT: H 42 ILE cc_start: 0.9466 (tt) cc_final: 0.9085 (mp) REVERT: H 95 TYR cc_start: 0.9015 (t80) cc_final: 0.8320 (t80) REVERT: H 121 LEU cc_start: 0.9289 (mm) cc_final: 0.9044 (mt) REVERT: H 141 TYR cc_start: 0.8283 (m-80) cc_final: 0.8057 (m-80) REVERT: I 39 LYS cc_start: 0.9199 (mptt) cc_final: 0.8807 (mmtm) REVERT: I 94 MET cc_start: 0.2273 (mmt) cc_final: 0.1755 (tpp) REVERT: J 49 MET cc_start: 0.9473 (mmm) cc_final: 0.8958 (mmm) REVERT: J 58 GLU cc_start: 0.9430 (mm-30) cc_final: 0.8272 (tm-30) REVERT: K 69 ASP cc_start: 0.8599 (p0) cc_final: 0.8064 (p0) REVERT: K 99 ASN cc_start: 0.9176 (p0) cc_final: 0.8747 (p0) REVERT: K 100 LEU cc_start: 0.9337 (mt) cc_final: 0.8982 (mt) REVERT: K 101 LEU cc_start: 0.9422 (tp) cc_final: 0.9110 (tp) REVERT: K 125 MET cc_start: 0.9382 (ptp) cc_final: 0.8791 (mtm) REVERT: K 135 PHE cc_start: 0.9198 (t80) cc_final: 0.8602 (t80) REVERT: L 27 LEU cc_start: 0.8603 (tp) cc_final: 0.7870 (tp) REVERT: M 52 VAL cc_start: 0.8120 (t) cc_final: 0.7772 (p) REVERT: N 27 ASP cc_start: 0.9693 (t0) cc_final: 0.9389 (t70) REVERT: N 82 ILE cc_start: 0.9210 (mt) cc_final: 0.8972 (mt) REVERT: N 88 LYS cc_start: 0.9342 (mttt) cc_final: 0.9133 (mmtm) REVERT: N 169 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8690 (mt-10) REVERT: O 467 MET cc_start: 0.3533 (mmp) cc_final: 0.3215 (mmp) REVERT: O 525 MET cc_start: -0.0343 (tpt) cc_final: -0.1192 (tpt) REVERT: O 527 MET cc_start: 0.5990 (tpt) cc_final: 0.5768 (tmm) outliers start: 1 outliers final: 0 residues processed: 792 average time/residue: 0.2674 time to fit residues: 348.9577 Evaluate side-chains 648 residues out of total 4879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 498 optimal weight: 50.0000 chunk 160 optimal weight: 0.9990 chunk 283 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 492 optimal weight: 3.9990 chunk 359 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 433 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 686 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** G 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN N 34 HIS O 451 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.111784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.074866 restraints weight = 191986.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075700 restraints weight = 145598.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076774 restraints weight = 123390.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077151 restraints weight = 107189.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.077419 restraints weight = 97385.839| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.934 44443 Z= 0.361 Angle : 0.684 20.328 60029 Z= 0.355 Chirality : 0.046 0.339 6174 Planarity : 0.005 0.224 7686 Dihedral : 14.094 166.614 7179 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.38 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.07 (0.11), residues: 5522 helix: 1.41 (0.11), residues: 2259 sheet: -0.51 (0.19), residues: 723 loop : -1.03 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 129 TYR 0.035 0.002 TYR G 53 PHE 0.040 0.002 PHE B 440 TRP 0.060 0.002 TRP G 166 HIS 0.015 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.01101 (44412) covalent geometry : angle 0.67830 (60002) hydrogen bonds : bond 0.03690 ( 2132) hydrogen bonds : angle 4.92979 ( 6059) metal coordination : bond 0.00623 ( 22) metal coordination : angle 4.31847 ( 27) Misc. bond : bond 0.00557 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11691.34 seconds wall clock time: 201 minutes 29.02 seconds (12089.02 seconds total)