Starting phenix.real_space_refine on Tue Aug 26 13:19:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9h_27964/08_2025/8e9h_27964.map" } resolution = 2.7 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= 0.036 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 32 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 230 5.16 5 C 23765 2.51 5 N 6268 2.21 5 O 6369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s 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: 36670 Number of models: 1 Model: "" Number of chains: 22 Chain: "O" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 896 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1338 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 168} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 198} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3051 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 21, 'TRANS': 385} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ASP:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1614 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 209} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 11, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5637 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 722} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 13, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 133 Chain: "F" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3170 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 404} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 13, 'GLN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "I" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1225 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 6, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "H" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2936 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "J" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1624 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "K" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 748 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4132 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 602} Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 15, 'HIS:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 256 Chain: "N" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3665 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 492} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "M" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3744 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 489} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'GLU:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'MQ9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'FES': 1, 'GTP': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'XP2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1152 SG CYS B 38 54.518 82.606 100.406 1.00 93.90 S ATOM 1146 SG CYS B 37 58.997 80.882 100.266 1.00 94.99 S ATOM 1868 SG CYS B 132 57.100 79.066 95.400 1.00 88.71 S ATOM 1658 SG CYS B 103 54.379 76.018 98.857 1.00 89.58 S ATOM 8627 SG CYS E 107 76.158 59.482 29.090 1.00115.90 S ATOM 8663 SG CYS E 112 79.151 60.143 26.901 1.00118.41 S ATOM 8905 SG CYS E 148 78.912 55.299 31.280 1.00117.44 S ATOM 8929 SG CYS E 152 81.668 56.105 29.448 1.00121.90 S ATOM 9803 SG CYS G 48 69.369 48.261 60.406 1.00 88.08 S ATOM 9878 SG CYS G 59 70.811 51.639 61.506 1.00 89.55 S ATOM 9904 SG CYS G 62 74.560 47.431 63.732 1.00 92.14 S ATOM 9995 SG CYS G 76 71.993 45.414 61.981 1.00 92.90 S ATOM 10276 SG CYS G 114 63.349 66.964 67.508 1.00 85.21 S ATOM 10337 SG CYS G 123 62.715 60.243 67.615 1.00 85.95 S ATOM 10297 SG CYS G 117 58.039 63.129 65.863 1.00 86.72 S ATOM 11029 SG CYS G 213 58.877 55.346 62.334 1.00 86.01 S ATOM 10674 SG CYS G 166 63.208 51.804 60.724 1.00 87.54 S ATOM 10653 SG CYS G 163 61.371 56.309 56.397 1.00 88.87 S ATOM 10696 SG CYS G 169 57.991 51.041 57.281 1.00 87.72 S ATOM 11223 SG CYS G 239 42.914 43.277 73.393 1.00 93.78 S ATOM 11269 SG CYS G 246 47.939 39.862 72.118 1.00 91.60 S ATOM 11490 SG CYS G 274 43.783 42.704 67.270 1.00 92.69 S ATOM 11248 SG CYS G 242 42.145 38.002 70.418 1.00 97.96 S ATOM 17594 SG CYS F 334 86.489 72.759 38.303 1.00115.98 S ATOM 18263 SG CYS F 426 84.616 75.522 36.871 1.00118.14 S ATOM 17757 SG CYS F 354 74.487 51.433 52.742 1.00 94.58 S ATOM 18076 SG CYS F 397 76.464 48.886 47.428 1.00 98.28 S ATOM 17777 SG CYS F 357 74.969 55.215 48.327 1.00 94.97 S ATOM 17738 SG CYS F 351 70.441 50.381 47.678 1.00 97.27 S ATOM 19064 SG CYS I 99 53.810 80.209 87.809 1.00 84.11 S ATOM 19082 SG CYS I 102 59.619 77.125 87.332 1.00 85.66 S ATOM 19100 SG CYS I 105 56.983 79.164 82.318 1.00 85.37 S ATOM 18788 SG CYS I 64 55.048 74.143 85.997 1.00 84.01 S ATOM 18758 SG CYS I 60 54.064 75.120 77.758 1.00 82.94 S ATOM 18735 SG CYS I 57 56.544 72.969 72.572 1.00 84.08 S ATOM 19128 SG CYS I 109 57.568 78.647 73.695 1.00 85.55 S ATOM 18717 SG CYS I 54 51.136 76.950 72.633 1.00 86.74 S Time building chain proxies: 7.65, per 1000 atoms: 0.21 Number of scatterers: 36670 At special positions: 0 Unit cell: (113.3, 147.526, 279.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 32 26.01 S 230 16.00 P 5 15.00 O 6369 8.00 N 6268 7.00 C 23765 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1000 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 152 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 107 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 112 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 148 " pdb=" FES G 801 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 59 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 48 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 62 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 76 " pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 103 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 37 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 132 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 38 " pdb=" SF4 F 503 " pdb="FE4 SF4 F 503 " - pdb=" SG CYS F 351 " pdb="FE2 SF4 F 503 " - pdb=" SG CYS F 397 " pdb="FE1 SF4 F 503 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 503 " - pdb=" SG CYS F 357 " pdb=" SF4 G 803 " pdb="FE3 SF4 G 803 " - pdb=" NE2 HIS G 110 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 117 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 123 " pdb=" SF4 G 804 " pdb="FE2 SF4 G 804 " - pdb=" SG CYS G 166 " pdb="FE3 SF4 G 804 " - pdb=" SG CYS G 163 " pdb="FE4 SF4 G 804 " - pdb=" SG CYS G 169 " pdb="FE1 SF4 G 804 " - pdb=" SG CYS G 213 " pdb=" SF4 G 805 " pdb="FE4 SF4 G 805 " - pdb=" SG CYS G 242 " pdb="FE2 SF4 G 805 " - pdb=" SG CYS G 246 " pdb="FE1 SF4 G 805 " - pdb=" SG CYS G 239 " pdb="FE3 SF4 G 805 " - pdb=" SG CYS G 274 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" NE2 HIS I 42 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 64 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 57 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 54 " Number of angles added : 93 Zn2+ tetrahedral coordination pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 426 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 421 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 334 " 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9152 Finding SS restraints... Secondary structure from input PDB file: 237 helices and 29 sheets defined 62.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'O' and resid 15 through 26 Processing helix chain 'O' and resid 44 through 54 Processing helix chain 'O' and resid 70 through 82 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 104 Processing helix chain 'O' and resid 115 through 128 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.537A pdb=" N GLU B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 155 through 171 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'A' and resid 4 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.552A pdb=" N ILE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.554A pdb=" N TRP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.617A pdb=" N GLY A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 116 Processing helix chain 'C' and resid 31 through 34 removed outlier: 3.996A pdb=" N ASN C 34 " --> pdb=" O MET C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 49 through 53 removed outlier: 3.995A pdb=" N HIS D 53 " --> pdb=" O PRO D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 86 removed outlier: 3.960A pdb=" N GLU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.539A pdb=" N PHE D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.827A pdb=" N ILE D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.739A pdb=" N MET D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 226 Proline residue: D 215 - end of helix removed outlier: 3.670A pdb=" N ASP D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 288 through 314 Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.686A pdb=" N THR D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'D' and resid 436 through 442 Processing helix chain 'E' and resid 26 through 42 Processing helix chain 'E' and resid 46 through 49 Processing helix chain 'E' and resid 50 through 62 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.541A pdb=" N PHE E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 116 through 129 Processing helix chain 'E' and resid 169 through 183 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 216 through 231 removed outlier: 4.211A pdb=" N THR E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 Processing helix chain 'G' and resid 92 through 109 removed outlier: 4.784A pdb=" N ASN G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 205 through 213 removed outlier: 3.902A pdb=" N THR G 209 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 281 through 286 removed outlier: 4.178A pdb=" N ALA G 284 " --> pdb=" O PHE G 281 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 286 " --> pdb=" O TYR G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 320 Processing helix chain 'G' and resid 333 through 347 Processing helix chain 'G' and resid 361 through 372 Processing helix chain 'G' and resid 380 through 385 Processing helix chain 'G' and resid 401 through 416 Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 444 through 452 Processing helix chain 'G' and resid 455 through 460 removed outlier: 3.558A pdb=" N ARG G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 474 Processing helix chain 'G' and resid 476 through 489 Processing helix chain 'G' and resid 499 through 507 removed outlier: 4.517A pdb=" N GLY G 503 " --> pdb=" O ALA G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 517 No H-bonds generated for 'chain 'G' and resid 515 through 517' Processing helix chain 'G' and resid 522 through 534 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 567 through 571 Processing helix chain 'G' and resid 573 through 584 Processing helix chain 'G' and resid 595 through 600 Processing helix chain 'G' and resid 609 through 613 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 657 through 669 Processing helix chain 'G' and resid 706 through 710 Processing helix chain 'G' and resid 712 through 718 Processing helix chain 'G' and resid 727 through 734 Processing helix chain 'G' and resid 775 through 780 Processing helix chain 'F' and resid 8 through 12 removed outlier: 4.012A pdb=" N PHE F 11 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 39 through 51 Processing helix chain 'F' and resid 61 through 68 Processing helix chain 'F' and resid 101 through 109 Processing helix chain 'F' and resid 109 through 125 removed outlier: 4.246A pdb=" N LEU F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 154 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 210 through 213 Processing helix chain 'F' and resid 220 through 225 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.782A pdb=" N TRP F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 355 through 373 Processing helix chain 'F' and resid 377 through 392 removed outlier: 3.950A pdb=" N ILE F 381 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 422 removed outlier: 4.339A pdb=" N ASP F 401 " --> pdb=" O CYS F 397 " (cutoff:3.500A) Proline residue: F 406 - end of helix removed outlier: 6.869A pdb=" N ASP F 416 " --> pdb=" O LYS F 412 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU F 417 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'I' and resid 4 through 7 Processing helix chain 'I' and resid 8 through 20 removed outlier: 3.744A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 157 through 164 Processing helix chain 'H' and resid 13 through 47 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 61 through 73 Processing helix chain 'H' and resid 82 through 101 Proline residue: H 90 - end of helix Proline residue: H 96 - end of helix removed outlier: 3.827A pdb=" N PHE H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 126 through 149 removed outlier: 3.952A pdb=" N TYR H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 141 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE H 142 " --> pdb=" O GLY H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 184 removed outlier: 5.085A pdb=" N ILE H 170 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 195 Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.837A pdb=" N LEU H 203 " --> pdb=" O TRP H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 219 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 239 Processing helix chain 'H' and resid 242 through 268 removed outlier: 3.650A pdb=" N PHE H 246 " --> pdb=" O SER H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 3.809A pdb=" N LEU H 280 " --> pdb=" O PHE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 312 removed outlier: 3.583A pdb=" N LEU H 292 " --> pdb=" O TRP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 327 Processing helix chain 'H' and resid 327 through 348 Processing helix chain 'H' and resid 350 through 375 Processing helix chain 'J' and resid 16 through 40 Processing helix chain 'J' and resid 42 through 64 Processing helix chain 'J' and resid 66 through 92 Processing helix chain 'J' and resid 106 through 127 Processing helix chain 'J' and resid 129 through 133 Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 144 through 156 Processing helix chain 'J' and resid 157 through 180 removed outlier: 3.819A pdb=" N SER J 165 " --> pdb=" O PHE J 161 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 186 Processing helix chain 'J' and resid 189 through 194 Processing helix chain 'J' and resid 231 through 235 removed outlier: 3.619A pdb=" N VAL J 235 " --> pdb=" O PRO J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 24 removed outlier: 4.048A pdb=" N LEU K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 53 Processing helix chain 'K' and resid 55 through 87 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'L' and resid 9 through 26 Proline residue: L 15 - end of helix removed outlier: 3.875A pdb=" N GLY L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 30 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 59 through 64 Processing helix chain 'L' and resid 87 through 112 removed outlier: 3.648A pdb=" N CYS L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 138 Processing helix chain 'L' and resid 140 through 160 Processing helix chain 'L' and resid 165 through 198 Processing helix chain 'L' and resid 201 through 209 Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 240 through 245 removed outlier: 3.516A pdb=" N MET L 245 " --> pdb=" O LEU L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 258 removed outlier: 3.558A pdb=" N ALA L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 271 removed outlier: 3.948A pdb=" N VAL L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 277 removed outlier: 3.842A pdb=" N LEU L 277 " --> pdb=" O PRO L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 303 removed outlier: 3.653A pdb=" N ALA L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 327 Processing helix chain 'L' and resid 328 through 360 removed outlier: 4.601A pdb=" N ALA L 333 " --> pdb=" O PRO L 329 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 376 removed outlier: 4.267A pdb=" N VAL L 375 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 392 Processing helix chain 'L' and resid 397 through 412 removed outlier: 3.997A pdb=" N SER L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 444 Processing helix chain 'L' and resid 459 through 482 Proline residue: L 465 - end of helix removed outlier: 5.595A pdb=" N GLY L 477 " --> pdb=" O SER L 473 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 491 Processing helix chain 'L' and resid 504 through 528 removed outlier: 3.707A pdb=" N VAL L 508 " --> pdb=" O PRO L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 548 Processing helix chain 'L' and resid 551 through 560 removed outlier: 3.515A pdb=" N PHE L 555 " --> pdb=" O TYR L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 560 through 578 Processing helix chain 'L' and resid 578 through 601 removed outlier: 3.811A pdb=" N ALA L 583 " --> pdb=" O VAL L 579 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN L 601 " --> pdb=" O LEU L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 614 Processing helix chain 'L' and resid 615 through 625 Processing helix chain 'N' and resid 7 through 31 Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 32 through 62 removed outlier: 4.390A pdb=" N TYR N 37 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Proline residue: N 38 - end of helix Processing helix chain 'N' and resid 78 through 100 Processing helix chain 'N' and resid 128 through 138 Processing helix chain 'N' and resid 143 through 161 Proline residue: N 159 - end of helix Processing helix chain 'N' and resid 163 through 182 Proline residue: N 177 - end of helix Processing helix chain 'N' and resid 188 through 222 Processing helix chain 'N' and resid 225 through 235 Processing helix chain 'N' and resid 241 through 259 Processing helix chain 'N' and resid 260 through 265 removed outlier: 4.508A pdb=" N SER N 265 " --> pdb=" O VAL N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 274 removed outlier: 4.172A pdb=" N ASP N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 300 removed outlier: 4.072A pdb=" N LYS N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 330 Proline residue: N 311 - end of helix removed outlier: 3.695A pdb=" N ALA N 328 " --> pdb=" O GLY N 324 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR N 330 " --> pdb=" O VAL N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 355 Processing helix chain 'N' and resid 357 through 383 Processing helix chain 'N' and resid 395 through 400 Processing helix chain 'N' and resid 401 through 406 Processing helix chain 'N' and resid 406 through 422 Processing helix chain 'N' and resid 426 through 442 Processing helix chain 'N' and resid 444 through 472 removed outlier: 3.865A pdb=" N TYR N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE N 461 " --> pdb=" O VAL N 457 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL N 465 " --> pdb=" O PHE N 461 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE N 466 " --> pdb=" O TYR N 462 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR N 472 " --> pdb=" O LEU N 468 " (cutoff:3.500A) Processing helix chain 'N' and resid 485 through 505 removed outlier: 3.504A pdb=" N THR N 489 " --> pdb=" O SER N 485 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY N 503 " --> pdb=" O THR N 499 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 516 removed outlier: 6.260A pdb=" N LEU N 512 " --> pdb=" O PRO N 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 25 Proline residue: M 15 - end of helix Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 29 through 55 Processing helix chain 'M' and resid 72 through 75 Processing helix chain 'M' and resid 83 through 104 Proline residue: M 98 - end of helix Processing helix chain 'M' and resid 106 through 111 removed outlier: 4.170A pdb=" N ARG M 110 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 116 Processing helix chain 'M' and resid 117 through 139 Processing helix chain 'M' and resid 141 through 152 Processing helix chain 'M' and resid 152 through 162 removed outlier: 3.828A pdb=" N MET M 156 " --> pdb=" O MET M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 199 Processing helix chain 'M' and resid 209 through 220 Processing helix chain 'M' and resid 225 through 244 Processing helix chain 'M' and resid 251 through 260 removed outlier: 4.653A pdb=" N ASP M 255 " --> pdb=" O ARG M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 270 Processing helix chain 'M' and resid 273 through 288 removed outlier: 3.761A pdb=" N THR M 277 " --> pdb=" O ASP M 273 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE M 288 " --> pdb=" O CYS M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 317 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 319 through 341 Processing helix chain 'M' and resid 343 through 375 Processing helix chain 'M' and resid 379 through 383 Processing helix chain 'M' and resid 385 through 390 removed outlier: 4.040A pdb=" N VAL M 389 " --> pdb=" O GLY M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 405 Processing helix chain 'M' and resid 410 through 427 removed outlier: 4.271A pdb=" N ILE M 414 " --> pdb=" O LEU M 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER M 415 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG M 426 " --> pdb=" O GLY M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 454 removed outlier: 4.177A pdb=" N ALA M 437 " --> pdb=" O PHE M 433 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU M 438 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL M 439 " --> pdb=" O ALA M 435 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR M 448 " --> pdb=" O TYR M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 492 Proline residue: M 481 - end of helix Processing helix chain 'M' and resid 493 through 512 removed outlier: 3.621A pdb=" N VAL M 499 " --> pdb=" O PRO M 495 " (cutoff:3.500A) Proline residue: M 502 - end of helix Processing sheet with id=AA1, first strand: chain 'O' and resid 37 through 42 removed outlier: 6.163A pdb=" N LEU O 7 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL O 40 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE O 9 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL O 42 " --> pdb=" O ILE O 9 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL O 11 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG O 8 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE O 61 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU O 10 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP O 63 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR O 12 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA O 60 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU O 91 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU O 62 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE O 88 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL O 110 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL O 90 " --> pdb=" O VAL O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.516A pdb=" N ILE B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 29 removed outlier: 5.277A pdb=" N ILE C 24 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 52 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 26 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 90 removed outlier: 4.958A pdb=" N LEU C 94 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 157 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 90 removed outlier: 4.958A pdb=" N LEU C 94 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 157 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AA7, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AA8, first strand: chain 'D' and resid 40 through 44 removed outlier: 6.457A pdb=" N GLU D 63 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 190 through 191 Processing sheet with id=AB1, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB2, first strand: chain 'D' and resid 373 through 381 Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.693A pdb=" N TYR E 102 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU E 144 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 104 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL E 146 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL E 106 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 23 through 28 removed outlier: 8.881A pdb=" N VAL G 86 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR G 19 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'G' and resid 182 through 185 Processing sheet with id=AB7, first strand: chain 'G' and resid 233 through 238 removed outlier: 5.589A pdb=" N ARG G 249 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG G 260 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP G 251 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 300 through 303 removed outlier: 6.375A pdb=" N VAL G 587 " --> pdb=" O VAL G 603 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE G 605 " --> pdb=" O VAL G 587 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER G 589 " --> pdb=" O PHE G 605 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 561 " --> pdb=" O VAL G 588 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU G 590 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 563 " --> pdb=" O LEU G 590 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY G 325 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY G 564 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU G 327 " --> pdb=" O GLY G 564 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ASP G 354 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 326 " --> pdb=" O ASP G 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 436 through 437 removed outlier: 6.184A pdb=" N THR G 389 " --> pdb=" O VAL G 464 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU G 466 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU G 391 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY G 468 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA G 393 " --> pdb=" O GLY G 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 513 through 514 Processing sheet with id=AC2, first strand: chain 'G' and resid 615 through 618 Processing sheet with id=AC3, first strand: chain 'G' and resid 693 through 699 removed outlier: 3.920A pdb=" N TRP G 699 " --> pdb=" O LEU G 767 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 175 Processing sheet with id=AC5, first strand: chain 'F' and resid 261 through 266 removed outlier: 6.664A pdb=" N ILE F 328 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER F 254 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP F 330 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'I' and resid 69 through 75 removed outlier: 6.448A pdb=" N ALA I 74 " --> pdb=" O GLY I 89 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY I 89 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 109 through 112 Processing sheet with id=AC9, first strand: chain 'L' and resid 65 through 73 removed outlier: 7.811A pdb=" N GLU L 67 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU L 86 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU L 69 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LEU L 84 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER L 71 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE L 82 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 385 through 386 Processing sheet with id=AD2, first strand: chain 'M' and resid 63 through 71 removed outlier: 5.460A pdb=" N PHE M 64 " --> pdb=" O VAL M 82 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL M 82 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP M 70 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR M 76 " --> pdb=" O TRP M 70 " (cutoff:3.500A) 2337 hydrogen bonds defined for protein. 6702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 14794 1.39 - 1.62: 22350 1.62 - 1.84: 337 1.84 - 2.06: 0 2.06 - 2.29: 92 Bond restraints: 37573 Sorted by residual: bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.485 1.382 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C50 XP2 L 701 " pdb=" O49 XP2 L 701 " ideal model delta sigma weight residual 1.344 1.437 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C39 XP2 L 701 " pdb=" O38 XP2 L 701 " ideal model delta sigma weight residual 1.348 1.438 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C28 XP2 L 701 " pdb=" C30 XP2 L 701 " ideal model delta sigma weight residual 1.561 1.480 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C58 XP2 L 701 " pdb=" C59 XP2 L 701 " ideal model delta sigma weight residual 1.526 1.603 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 37568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 50801 2.32 - 4.65: 650 4.65 - 6.97: 32 6.97 - 9.30: 7 9.30 - 11.62: 4 Bond angle restraints: 51494 Sorted by residual: angle pdb=" N PRO E 156 " pdb=" CA PRO E 156 " pdb=" CB PRO E 156 " ideal model delta sigma weight residual 103.25 95.01 8.24 1.05e+00 9.07e-01 6.17e+01 angle pdb=" N ARG J 197 " pdb=" CA ARG J 197 " pdb=" C ARG J 197 " ideal model delta sigma weight residual 110.80 100.66 10.14 2.13e+00 2.20e-01 2.26e+01 angle pdb=" C SER H 243 " pdb=" CA SER H 243 " pdb=" CB SER H 243 " ideal model delta sigma weight residual 115.89 110.21 5.68 1.32e+00 5.74e-01 1.85e+01 angle pdb=" CA PHE J 198 " pdb=" CB PHE J 198 " pdb=" CG PHE J 198 " ideal model delta sigma weight residual 113.80 109.85 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" N ILE L 200 " pdb=" CA ILE L 200 " pdb=" C ILE L 200 " ideal model delta sigma weight residual 113.53 109.71 3.82 9.80e-01 1.04e+00 1.52e+01 ... (remaining 51489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.65: 21622 31.65 - 63.30: 291 63.30 - 94.95: 34 94.95 - 126.60: 3 126.60 - 158.24: 3 Dihedral angle restraints: 21953 sinusoidal: 7609 harmonic: 14344 Sorted by residual: dihedral pdb=" C8 GTP G 802 " pdb=" C1' GTP G 802 " pdb=" N9 GTP G 802 " pdb=" O4' GTP G 802 " ideal model delta sinusoidal sigma weight residual 104.59 -97.16 -158.24 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O3A GTP G 802 " pdb=" O3B GTP G 802 " pdb=" PB GTP G 802 " pdb=" PG GTP G 802 " ideal model delta sinusoidal sigma weight residual -56.21 88.96 -145.17 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" CA MET D 45 " pdb=" C MET D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 21950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4851 0.046 - 0.092: 1034 0.092 - 0.138: 261 0.138 - 0.184: 7 0.184 - 0.230: 4 Chirality restraints: 6157 Sorted by residual: chirality pdb=" C73 XP2 L 701 " pdb=" C71 XP2 L 701 " pdb=" C74 XP2 L 701 " pdb=" O76 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ARG J 197 " pdb=" N ARG J 197 " pdb=" C ARG J 197 " pdb=" CB ARG J 197 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C11 XP2 L 701 " pdb=" C12 XP2 L 701 " pdb=" C26 XP2 L 701 " pdb=" O10 XP2 L 701 " both_signs ideal model delta sigma weight residual False 2.38 2.57 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 6154 not shown) Planarity restraints: 6510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 MQ9 D 501 " -0.152 2.00e-02 2.50e+03 2.24e-01 1.75e+03 pdb=" C2 MQ9 D 501 " -0.036 2.00e-02 2.50e+03 pdb=" C3 MQ9 D 501 " -0.032 2.00e-02 2.50e+03 pdb=" C3A MQ9 D 501 " 0.087 2.00e-02 2.50e+03 pdb=" C3B MQ9 D 501 " 0.186 2.00e-02 2.50e+03 pdb=" C3C MQ9 D 501 " 0.179 2.00e-02 2.50e+03 pdb=" C3D MQ9 D 501 " 0.071 2.00e-02 2.50e+03 pdb=" C4 MQ9 D 501 " -0.151 2.00e-02 2.50e+03 pdb=" C5 MQ9 D 501 " 0.076 2.00e-02 2.50e+03 pdb=" C5M MQ9 D 501 " 0.294 2.00e-02 2.50e+03 pdb=" C6 MQ9 D 501 " 0.077 2.00e-02 2.50e+03 pdb=" C7 MQ9 D 501 " 0.288 2.00e-02 2.50e+03 pdb=" O1 MQ9 D 501 " -0.434 2.00e-02 2.50e+03 pdb=" O4 MQ9 D 501 " -0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 MQ9 D 501 " 0.151 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C11 MQ9 D 501 " 0.125 2.00e-02 2.50e+03 pdb=" C7 MQ9 D 501 " 0.345 2.00e-02 2.50e+03 pdb=" C8 MQ9 D 501 " -0.515 2.00e-02 2.50e+03 pdb=" C9 MQ9 D 501 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 MQ9 D 501 " -0.268 2.00e-02 2.50e+03 2.25e-01 6.32e+02 pdb=" C33 MQ9 D 501 " 0.377 2.00e-02 2.50e+03 pdb=" C34 MQ9 D 501 " 0.078 2.00e-02 2.50e+03 pdb=" C35 MQ9 D 501 " -0.180 2.00e-02 2.50e+03 pdb=" C36 MQ9 D 501 " -0.008 2.00e-02 2.50e+03 ... (remaining 6507 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 65 2.36 - 3.00: 23343 3.00 - 3.63: 60309 3.63 - 4.27: 93393 4.27 - 4.90: 157118 Nonbonded interactions: 334228 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O TRP H 325 " model vdw 1.727 3.040 nonbonded pdb=" OE2 GLU F 372 " pdb="ZN ZN F 502 " model vdw 1.838 2.230 nonbonded pdb=" OG1 THR F 270 " pdb=" OE1 GLU F 273 " model vdw 1.949 3.040 nonbonded pdb=" OG1 THR B 63 " pdb=" OE1 GLN B 66 " model vdw 2.010 3.040 nonbonded pdb=" OE2 GLU B 58 " pdb=" NE ARG H 40 " model vdw 2.065 3.120 ... (remaining 334223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.170 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: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 38.480 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.008 0.833 37615 Z= 0.629 Angle : 0.822 63.307 51587 Z= 0.363 Chirality : 0.040 0.230 6157 Planarity : 0.007 0.295 6510 Dihedral : 11.982 158.244 12801 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 0.14 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.08 (0.12), residues: 5028 helix: 1.37 (0.10), residues: 2826 sheet: 0.06 (0.31), residues: 296 loop : -0.04 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.055 0.002 TYR N 367 PHE 0.034 0.002 PHE N 205 TRP 0.024 0.001 TRP I 62 HIS 0.013 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00509 (37573) covalent geometry : angle 0.64341 (51494) hydrogen bonds : bond 0.12623 ( 2317) hydrogen bonds : angle 6.36259 ( 6702) metal coordination : bond 0.03121 ( 40) metal coordination : angle 12.07963 ( 93) Misc. bond : bond 0.79179 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.253 Fit side-chains REVERT: D 320 MET cc_start: 0.8708 (tpp) cc_final: 0.8499 (tpt) REVERT: D 437 MET cc_start: 0.9149 (mmm) cc_final: 0.8854 (mmm) REVERT: G 701 MET cc_start: 0.9012 (mmm) cc_final: 0.8806 (mmp) REVERT: F 42 ASP cc_start: 0.8994 (m-30) cc_final: 0.8767 (m-30) REVERT: F 408 MET cc_start: 0.9148 (mtp) cc_final: 0.8797 (mtp) REVERT: H 186 MET cc_start: 0.9258 (mtp) cc_final: 0.8898 (mtm) REVERT: L 112 MET cc_start: 0.9549 (mmm) cc_final: 0.9323 (mmm) REVERT: L 193 MET cc_start: 0.8971 (mtp) cc_final: 0.8751 (mtp) REVERT: L 441 MET cc_start: 0.9145 (mtp) cc_final: 0.8900 (mtp) REVERT: M 135 MET cc_start: 0.9238 (tpt) cc_final: 0.8643 (tpp) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.6614 time to fit residues: 127.5653 Evaluate side-chains 153 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.1980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN C 178 HIS D 108 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 GLN G 643 HIS ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.036289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.029840 restraints weight = 265086.075| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.37 r_work: 0.2860 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37615 Z= 0.161 Angle : 0.796 67.079 51587 Z= 0.311 Chirality : 0.042 0.247 6157 Planarity : 0.005 0.131 6510 Dihedral : 7.249 150.290 5623 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 0.37 % Allowed : 3.92 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.31 (0.12), residues: 5028 helix: 1.58 (0.10), residues: 2852 sheet: 0.08 (0.31), residues: 296 loop : 0.02 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 498 TYR 0.032 0.002 TYR N 367 PHE 0.031 0.002 PHE L 345 TRP 0.014 0.001 TRP I 62 HIS 0.010 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00350 (37573) covalent geometry : angle 0.60428 (51494) hydrogen bonds : bond 0.04483 ( 2317) hydrogen bonds : angle 5.16494 ( 6702) metal coordination : bond 0.01769 ( 40) metal coordination : angle 12.20694 ( 93) Misc. bond : bond 0.01219 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.528 Fit side-chains REVERT: A 1 MET cc_start: 0.7438 (tpt) cc_final: 0.7202 (tpp) REVERT: D 437 MET cc_start: 0.9222 (mmm) cc_final: 0.8877 (mmm) REVERT: F 42 ASP cc_start: 0.9307 (m-30) cc_final: 0.9105 (m-30) REVERT: F 408 MET cc_start: 0.9536 (mtp) cc_final: 0.9280 (mtp) outliers start: 13 outliers final: 0 residues processed: 157 average time/residue: 0.8370 time to fit residues: 158.5529 Evaluate side-chains 152 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 139 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 0.0670 chunk 327 optimal weight: 6.9990 chunk 375 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 356 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 777 HIS ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.035743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.029219 restraints weight = 267679.472| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.36 r_work: 0.2832 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 37615 Z= 0.219 Angle : 0.784 64.079 51587 Z= 0.304 Chirality : 0.042 0.247 6157 Planarity : 0.005 0.115 6510 Dihedral : 6.843 152.969 5621 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 0.78 % Allowed : 5.80 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.38 (0.12), residues: 5028 helix: 1.64 (0.10), residues: 2839 sheet: 0.17 (0.31), residues: 308 loop : 0.04 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 127 TYR 0.025 0.002 TYR N 367 PHE 0.030 0.002 PHE L 345 TRP 0.014 0.001 TRP L 148 HIS 0.008 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00497 (37573) covalent geometry : angle 0.59248 (51494) hydrogen bonds : bond 0.04437 ( 2317) hydrogen bonds : angle 4.99493 ( 6702) metal coordination : bond 0.02885 ( 40) metal coordination : angle 12.12237 ( 93) Misc. bond : bond 0.00480 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.490 Fit side-chains REVERT: O 29 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8282 (mtp85) REVERT: A 1 MET cc_start: 0.7330 (tpt) cc_final: 0.7015 (tpp) REVERT: D 437 MET cc_start: 0.9316 (mmm) cc_final: 0.9107 (mmm) REVERT: E 159 MET cc_start: 0.9239 (mmm) cc_final: 0.8869 (mmm) REVERT: G 294 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.9002 (mmm) REVERT: F 38 MET cc_start: 0.8635 (mtm) cc_final: 0.8275 (ptm) REVERT: F 42 ASP cc_start: 0.9318 (m-30) cc_final: 0.9115 (m-30) REVERT: F 408 MET cc_start: 0.9521 (mtp) cc_final: 0.9275 (mtp) REVERT: L 112 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9052 (mmm) REVERT: L 193 MET cc_start: 0.9192 (mtm) cc_final: 0.8990 (mtp) REVERT: N 321 MET cc_start: 0.9323 (mtm) cc_final: 0.8969 (mtm) REVERT: N 469 MET cc_start: 0.9195 (mtp) cc_final: 0.8904 (mtm) REVERT: M 135 MET cc_start: 0.9420 (tpp) cc_final: 0.9074 (tpp) outliers start: 27 outliers final: 5 residues processed: 163 average time/residue: 0.7395 time to fit residues: 146.6489 Evaluate side-chains 159 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 277 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 770 ASN ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.036051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.029579 restraints weight = 265648.469| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.36 r_work: 0.2853 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 37615 Z= 0.162 Angle : 0.756 61.518 51587 Z= 0.286 Chirality : 0.041 0.236 6157 Planarity : 0.005 0.106 6510 Dihedral : 6.545 151.942 5621 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 0.84 % Allowed : 7.21 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.45 (0.12), residues: 5028 helix: 1.71 (0.10), residues: 2833 sheet: 0.36 (0.31), residues: 300 loop : 0.02 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 127 TYR 0.023 0.001 TYR M 444 PHE 0.031 0.001 PHE L 345 TRP 0.014 0.001 TRP L 148 HIS 0.009 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00363 (37573) covalent geometry : angle 0.55827 (51494) hydrogen bonds : bond 0.04095 ( 2317) hydrogen bonds : angle 4.86959 ( 6702) metal coordination : bond 0.02071 ( 40) metal coordination : angle 12.03663 ( 93) Misc. bond : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.535 Fit side-chains REVERT: O 29 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: E 159 MET cc_start: 0.9195 (mmm) cc_final: 0.8859 (mmm) REVERT: G 73 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.9176 (mmm) REVERT: G 294 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9022 (mmm) REVERT: F 38 MET cc_start: 0.8640 (mtm) cc_final: 0.8325 (ptm) REVERT: F 42 ASP cc_start: 0.9321 (m-30) cc_final: 0.9110 (m-30) REVERT: N 321 MET cc_start: 0.9240 (mtm) cc_final: 0.8894 (mtm) REVERT: M 135 MET cc_start: 0.9427 (tpp) cc_final: 0.9106 (tpp) outliers start: 29 outliers final: 6 residues processed: 168 average time/residue: 0.6676 time to fit residues: 137.7893 Evaluate side-chains 160 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 50 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 346 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 228 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.036681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.030260 restraints weight = 263961.400| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.39 r_work: 0.2891 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37615 Z= 0.117 Angle : 0.713 54.360 51587 Z= 0.270 Chirality : 0.040 0.240 6157 Planarity : 0.004 0.097 6510 Dihedral : 6.278 151.320 5621 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Rotamer: Outliers : 0.92 % Allowed : 8.07 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.53 (0.12), residues: 5028 helix: 1.78 (0.10), residues: 2847 sheet: 0.29 (0.31), residues: 306 loop : 0.03 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 383 TYR 0.024 0.001 TYR M 444 PHE 0.030 0.001 PHE L 345 TRP 0.014 0.001 TRP L 148 HIS 0.007 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00252 (37573) covalent geometry : angle 0.53054 (51494) hydrogen bonds : bond 0.03775 ( 2317) hydrogen bonds : angle 4.71860 ( 6702) metal coordination : bond 0.01303 ( 40) metal coordination : angle 11.23098 ( 93) Misc. bond : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.333 Fit side-chains REVERT: D 247 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9364 (mmm) REVERT: G 73 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9183 (mmm) REVERT: F 38 MET cc_start: 0.8624 (mtm) cc_final: 0.8411 (ptp) REVERT: F 42 ASP cc_start: 0.9260 (m-30) cc_final: 0.9041 (m-30) REVERT: L 132 MET cc_start: 0.8987 (tpt) cc_final: 0.8777 (ttt) REVERT: N 321 MET cc_start: 0.9181 (mtm) cc_final: 0.8868 (mtm) REVERT: M 135 MET cc_start: 0.9308 (tpp) cc_final: 0.8977 (tpp) outliers start: 32 outliers final: 7 residues processed: 171 average time/residue: 0.6679 time to fit residues: 139.9726 Evaluate side-chains 162 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 305 optimal weight: 6.9990 chunk 439 optimal weight: 3.9990 chunk 469 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 432 optimal weight: 0.9990 chunk 312 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 478 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.035866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.029351 restraints weight = 266415.726| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.37 r_work: 0.2845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 37615 Z= 0.206 Angle : 0.751 54.808 51587 Z= 0.289 Chirality : 0.042 0.241 6157 Planarity : 0.005 0.096 6510 Dihedral : 6.260 152.958 5621 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 1.01 % Allowed : 9.03 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.55 (0.12), residues: 5028 helix: 1.79 (0.10), residues: 2838 sheet: 0.49 (0.32), residues: 291 loop : 0.03 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 127 TYR 0.041 0.002 TYR G 644 PHE 0.029 0.001 PHE L 345 TRP 0.013 0.001 TRP N 309 HIS 0.008 0.001 HIS G 643 Details of bonding type rmsd covalent geometry : bond 0.00467 (37573) covalent geometry : angle 0.57351 (51494) hydrogen bonds : bond 0.04039 ( 2317) hydrogen bonds : angle 4.74545 ( 6702) metal coordination : bond 0.02708 ( 40) metal coordination : angle 11.43973 ( 93) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.351 Fit side-chains REVERT: O 29 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.9006 (ttm-80) REVERT: B 25 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8868 (ptpp) REVERT: G 73 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9184 (mmm) REVERT: G 242 CYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9069 (p) REVERT: G 294 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9060 (mmm) REVERT: F 38 MET cc_start: 0.8642 (mtm) cc_final: 0.8293 (ptm) REVERT: M 135 MET cc_start: 0.9387 (tpp) cc_final: 0.9098 (tpp) REVERT: M 152 MET cc_start: 0.9351 (ptt) cc_final: 0.9095 (ptp) outliers start: 35 outliers final: 10 residues processed: 176 average time/residue: 0.6374 time to fit residues: 137.5583 Evaluate side-chains 166 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 396 MET Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 496 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 477 optimal weight: 6.9990 chunk 484 optimal weight: 0.8980 chunk 388 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 103 optimal weight: 0.0980 chunk 490 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.036006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029522 restraints weight = 265920.103| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.36 r_work: 0.2855 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 37615 Z= 0.169 Angle : 0.735 53.087 51587 Z= 0.281 Chirality : 0.041 0.237 6157 Planarity : 0.004 0.093 6510 Dihedral : 6.199 152.950 5621 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.78 % Allowed : 9.78 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.58 (0.12), residues: 5028 helix: 1.81 (0.10), residues: 2834 sheet: 0.50 (0.32), residues: 291 loop : 0.07 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 127 TYR 0.034 0.001 TYR G 644 PHE 0.030 0.001 PHE L 345 TRP 0.013 0.001 TRP H 307 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00383 (37573) covalent geometry : angle 0.55667 (51494) hydrogen bonds : bond 0.03937 ( 2317) hydrogen bonds : angle 4.72501 ( 6702) metal coordination : bond 0.02239 ( 40) metal coordination : angle 11.31499 ( 93) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.382 Fit side-chains REVERT: B 25 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8867 (ptpp) REVERT: G 73 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9216 (mmm) REVERT: G 242 CYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9061 (p) REVERT: F 38 MET cc_start: 0.8604 (mtm) cc_final: 0.8284 (ptm) REVERT: H 186 MET cc_start: 0.9547 (mtp) cc_final: 0.9307 (mtm) REVERT: L 132 MET cc_start: 0.9090 (tpt) cc_final: 0.8817 (ttt) REVERT: M 135 MET cc_start: 0.9367 (tpp) cc_final: 0.9033 (tpp) outliers start: 27 outliers final: 12 residues processed: 174 average time/residue: 0.7074 time to fit residues: 150.8204 Evaluate side-chains 167 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 342 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 208 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 461 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 398 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 346 optimal weight: 0.9990 chunk 392 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN M 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.036528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.030103 restraints weight = 263837.416| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.37 r_work: 0.2888 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 37615 Z= 0.122 Angle : 0.709 49.260 51587 Z= 0.270 Chirality : 0.040 0.235 6157 Planarity : 0.004 0.087 6510 Dihedral : 6.039 151.967 5621 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.78 % Allowed : 10.06 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.63 (0.12), residues: 5028 helix: 1.86 (0.10), residues: 2846 sheet: 0.35 (0.31), residues: 306 loop : 0.08 (0.16), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 383 TYR 0.034 0.001 TYR G 644 PHE 0.030 0.001 PHE L 345 TRP 0.014 0.001 TRP L 148 HIS 0.007 0.001 HIS G 643 Details of bonding type rmsd covalent geometry : bond 0.00271 (37573) covalent geometry : angle 0.53710 (51494) hydrogen bonds : bond 0.03702 ( 2317) hydrogen bonds : angle 4.66486 ( 6702) metal coordination : bond 0.01455 ( 40) metal coordination : angle 10.89994 ( 93) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.183 Fit side-chains REVERT: G 40 MET cc_start: 0.8911 (ttm) cc_final: 0.8676 (mtm) REVERT: G 73 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9178 (mmm) REVERT: G 242 CYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9038 (p) REVERT: F 38 MET cc_start: 0.8610 (mtm) cc_final: 0.8349 (ptm) REVERT: L 132 MET cc_start: 0.9101 (tpt) cc_final: 0.8857 (ttt) REVERT: M 135 MET cc_start: 0.9302 (tpp) cc_final: 0.8965 (tpp) outliers start: 27 outliers final: 10 residues processed: 176 average time/residue: 0.6587 time to fit residues: 141.4451 Evaluate side-chains 164 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 207 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 482 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 380 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 167 ASN M 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.035419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028858 restraints weight = 267622.032| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.37 r_work: 0.2817 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 37615 Z= 0.290 Angle : 0.797 51.531 51587 Z= 0.316 Chirality : 0.044 0.243 6157 Planarity : 0.005 0.087 6510 Dihedral : 6.167 154.472 5621 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 0.72 % Allowed : 10.18 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.52 (0.12), residues: 5028 helix: 1.73 (0.10), residues: 2845 sheet: 0.49 (0.32), residues: 291 loop : 0.06 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 75 TYR 0.053 0.002 TYR G 644 PHE 0.030 0.002 PHE L 345 TRP 0.014 0.001 TRP N 309 HIS 0.008 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00659 (37573) covalent geometry : angle 0.62670 (51494) hydrogen bonds : bond 0.04273 ( 2317) hydrogen bonds : angle 4.81251 ( 6702) metal coordination : bond 0.03548 ( 40) metal coordination : angle 11.62961 ( 93) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.420 Fit side-chains REVERT: G 242 CYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9114 (p) REVERT: G 294 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9091 (mmm) REVERT: F 38 MET cc_start: 0.8725 (mtm) cc_final: 0.8359 (ptm) REVERT: L 132 MET cc_start: 0.9120 (tpt) cc_final: 0.8843 (ttt) REVERT: M 135 MET cc_start: 0.9409 (tpp) cc_final: 0.9149 (tpp) outliers start: 25 outliers final: 12 residues processed: 170 average time/residue: 0.6699 time to fit residues: 138.4187 Evaluate side-chains 165 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 396 MET Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 169 optimal weight: 5.9990 chunk 423 optimal weight: 0.0980 chunk 375 optimal weight: 20.0000 chunk 429 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 416 optimal weight: 0.9990 chunk 334 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 123 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.036495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.030059 restraints weight = 263328.617| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.38 r_work: 0.2881 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 37615 Z= 0.119 Angle : 0.723 49.208 51587 Z= 0.277 Chirality : 0.040 0.232 6157 Planarity : 0.004 0.080 6510 Dihedral : 6.033 152.440 5621 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.43 % Allowed : 10.35 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.61 (0.12), residues: 5028 helix: 1.83 (0.10), residues: 2843 sheet: 0.51 (0.32), residues: 291 loop : 0.08 (0.15), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 383 TYR 0.031 0.001 TYR G 644 PHE 0.030 0.001 PHE L 345 TRP 0.014 0.001 TRP H 299 HIS 0.004 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00260 (37573) covalent geometry : angle 0.55145 (51494) hydrogen bonds : bond 0.03765 ( 2317) hydrogen bonds : angle 4.70760 ( 6702) metal coordination : bond 0.01414 ( 40) metal coordination : angle 11.03842 ( 93) Misc. bond : bond 0.00055 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10056 Ramachandran restraints generated. 5028 Oldfield, 0 Emsley, 5028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.101 Fit side-chains REVERT: G 40 MET cc_start: 0.8969 (ttm) cc_final: 0.8719 (mtm) REVERT: G 242 CYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9114 (p) REVERT: F 38 MET cc_start: 0.8673 (mtm) cc_final: 0.8325 (ptm) REVERT: H 186 MET cc_start: 0.9499 (mtp) cc_final: 0.9227 (mtm) REVERT: L 561 MET cc_start: 0.7918 (ttt) cc_final: 0.7685 (ttm) REVERT: N 97 MET cc_start: 0.9348 (mtm) cc_final: 0.9128 (mtp) REVERT: N 140 MET cc_start: 0.9030 (ptp) cc_final: 0.8722 (mtm) REVERT: M 135 MET cc_start: 0.9317 (tpp) cc_final: 0.8970 (tpp) outliers start: 15 outliers final: 11 residues processed: 166 average time/residue: 0.6469 time to fit residues: 132.1668 Evaluate side-chains 164 residues out of total 3938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 153 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 465 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 215 optimal weight: 0.0870 chunk 102 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 396 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.035929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029432 restraints weight = 264286.063| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.36 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 37615 Z= 0.194 Angle : 0.753 50.062 51587 Z= 0.291 Chirality : 0.041 0.240 6157 Planarity : 0.004 0.079 6510 Dihedral : 6.035 153.129 5621 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 0.58 % Allowed : 10.38 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.62 (0.12), residues: 5028 helix: 1.83 (0.10), residues: 2843 sheet: 0.56 (0.32), residues: 289 loop : 0.09 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 127 TYR 0.041 0.001 TYR G 644 PHE 0.030 0.001 PHE L 345 TRP 0.014 0.001 TRP N 309 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00441 (37573) covalent geometry : angle 0.58413 (51494) hydrogen bonds : bond 0.03946 ( 2317) hydrogen bonds : angle 4.71641 ( 6702) metal coordination : bond 0.02490 ( 40) metal coordination : angle 11.20172 ( 93) Misc. bond : bond 0.00066 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11365.32 seconds wall clock time: 194 minutes 21.48 seconds (11661.48 seconds total)