Starting phenix.real_space_refine on Sat Jun 21 20:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857.map" model { file = "/net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z99_39857/06_2025/8z99_39857_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 100 5.49 5 S 109 5.16 5 C 15710 2.51 5 N 4456 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25517 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1232 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1539 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1539 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1547 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1492 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1364 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "H" Number of atoms: 4649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4649 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 563} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "I" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1341 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1541 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 10 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "L" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1315 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1130 Classifications: {'RNA': 54} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 16, 'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 26} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 986 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 17} Link IDs: {'rna2p': 6, 'rna3p': 39} Chain breaks: 1 Chain: "P" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1437 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 395 SG CYS A 71 33.118 57.429 200.162 1.00161.78 S ATOM 469 SG CYS A 81 30.927 58.339 198.246 1.00159.75 S ATOM 490 SG CYS A 84 30.672 60.174 201.669 1.00149.80 S ATOM 510 SG CYS A 87 33.113 61.491 199.598 1.00149.15 S ATOM 1780 SG CYS B 71 24.150 81.825 176.514 1.00124.48 S ATOM 1854 SG CYS B 81 22.653 84.391 174.604 1.00107.67 S ATOM 1875 SG CYS B 84 24.493 85.862 177.611 1.00102.77 S ATOM 1895 SG CYS B 87 26.534 84.639 175.495 1.00108.74 S ATOM 3323 SG CYS C 71 38.938 101.496 152.964 1.00 98.61 S ATOM 3397 SG CYS C 81 38.975 104.407 150.372 1.00 95.67 S ATOM 3418 SG CYS C 84 41.645 104.192 153.069 1.00100.30 S ATOM 3438 SG CYS C 87 41.730 101.572 150.714 1.00 89.57 S ATOM 4862 SG CYS D 71 75.790 79.469 104.562 1.00106.91 S ATOM 4936 SG CYS D 81 78.737 78.989 101.504 1.00109.51 S ATOM 4957 SG CYS D 84 78.833 77.596 104.568 1.00103.52 S ATOM 4977 SG CYS D 87 75.428 76.863 102.657 1.00 80.08 S ATOM 6409 SG CYS E 71 67.986 55.776 81.872 1.00110.28 S ATOM 6483 SG CYS E 81 67.716 52.507 79.525 1.00121.72 S ATOM 6504 SG CYS E 84 66.995 52.133 82.407 1.00109.53 S ATOM 6524 SG CYS E 87 64.465 54.399 80.968 1.00 93.24 S ATOM 7937 SG CYS F 71 42.490 47.540 59.953 1.00131.25 S ATOM 8011 SG CYS F 81 40.026 45.482 57.706 1.00146.59 S ATOM 8032 SG CYS F 84 38.637 47.103 61.092 1.00137.55 S ATOM 8052 SG CYS F 87 39.939 49.074 58.544 1.00128.62 S ATOM 16786 SG CYS J 71 62.557 100.371 128.220 1.00102.49 S ATOM 16860 SG CYS J 81 65.009 102.070 125.527 1.00 93.19 S ATOM 16881 SG CYS J 84 66.286 99.899 128.519 1.00102.90 S ATOM 16901 SG CYS J 87 64.272 98.305 125.967 1.00 90.58 S ATOM 24602 SG CYS P 71 21.542 61.079 36.075 1.00184.40 S ATOM 24681 SG CYS P 84 20.075 64.223 37.225 1.00187.62 S ATOM 24701 SG CYS P 87 22.492 64.648 35.628 1.00179.18 S Time building chain proxies: 16.68, per 1000 atoms: 0.65 Number of scatterers: 25517 At special positions: 0 Unit cell: (93.1, 127.3, 233.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 109 16.00 P 100 15.00 O 5133 8.00 N 4456 7.00 C 15710 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=0, symmetry=0 Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 87 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 71 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 84 " Number of angles added : 42 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5692 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 39 sheets defined 36.2% alpha, 18.7% beta 26 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 10.13 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 51 through 67 removed outlier: 4.019A pdb=" N LYS B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.561A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'C' and resid 24 through 31 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.555A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'D' and resid 24 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.639A pdb=" N ILE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 113' Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 196 through 200 removed outlier: 3.566A pdb=" N LYS E 200 " --> pdb=" O ARG E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 removed outlier: 3.728A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 66 removed outlier: 3.600A pdb=" N ALA F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 109 through 112 Processing helix chain 'F' and resid 156 through 172 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.704A pdb=" N LEU G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 53 removed outlier: 4.246A pdb=" N SER G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 141 Processing helix chain 'H' and resid 40 through 53 removed outlier: 3.518A pdb=" N ILE H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 107 Processing helix chain 'H' and resid 114 through 124 removed outlier: 3.972A pdb=" N ILE H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.818A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 245 Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 273 through 278 Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 321 through 333 removed outlier: 4.382A pdb=" N ASN H 325 " --> pdb=" O GLY H 321 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS H 326 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 333 " --> pdb=" O GLN H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 356 Processing helix chain 'H' and resid 375 through 385 Processing helix chain 'H' and resid 399 through 413 Processing helix chain 'H' and resid 470 through 481 removed outlier: 3.900A pdb=" N PHE H 474 " --> pdb=" O ASP H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 593 removed outlier: 3.887A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 593 " --> pdb=" O SER H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 603 Processing helix chain 'I' and resid 470 through 489 removed outlier: 3.997A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 489 " --> pdb=" O MET I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 541 through 554 removed outlier: 3.510A pdb=" N ALA I 545 " --> pdb=" O GLY I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 593 removed outlier: 3.966A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR I 593 " --> pdb=" O SER I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 604 removed outlier: 4.132A pdb=" N ASN I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 156 through 172 removed outlier: 3.820A pdb=" N SER J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 86 through 104 removed outlier: 3.613A pdb=" N LYS K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG K 94 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU K 95 " --> pdb=" O GLU K 91 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 122 Processing helix chain 'K' and resid 377 through 386 removed outlier: 3.841A pdb=" N LEU K 386 " --> pdb=" O TYR K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 413 removed outlier: 3.954A pdb=" N ARG K 409 " --> pdb=" O ILE K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 489 removed outlier: 3.740A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER K 487 " --> pdb=" O ASN K 483 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE K 489 " --> pdb=" O MET K 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 Processing helix chain 'K' and resid 541 through 554 Processing helix chain 'K' and resid 572 through 593 removed outlier: 3.696A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR K 593 " --> pdb=" O SER K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 486 Processing helix chain 'L' and resid 509 through 523 Processing helix chain 'L' and resid 527 through 541 Processing helix chain 'L' and resid 541 through 554 Processing helix chain 'L' and resid 572 through 593 removed outlier: 3.929A pdb=" N GLU L 577 " --> pdb=" O ASP L 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 603 Processing helix chain 'P' and resid 24 through 32 Processing helix chain 'P' and resid 51 through 67 Processing helix chain 'P' and resid 84 through 91 Processing helix chain 'P' and resid 109 through 114 removed outlier: 3.691A pdb=" N ILE P 113 " --> pdb=" O THR P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 170 removed outlier: 3.759A pdb=" N LEU P 158 " --> pdb=" O GLN P 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.745A pdb=" N TYR B 9 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 122 removed outlier: 3.783A pdb=" N ASP B 131 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 122 removed outlier: 3.562A pdb=" N ARG C 121 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 131 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.492A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 Processing sheet with id=AB6, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 119 Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 61 Processing sheet with id=AC1, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC3, first strand: chain 'G' and resid 180 through 181 removed outlier: 4.101A pdb=" N LYS G 206 " --> pdb=" O ILE G 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.555A pdb=" N LYS H 140 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU H 158 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N VAL H 153 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY H 168 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 162 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU H 195 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 396 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU H 194 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 225 through 226 removed outlier: 6.832A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL H 251 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 435 through 436 Processing sheet with id=AC8, first strand: chain 'H' and resid 435 through 436 removed outlier: 4.556A pdb=" N ARG H 451 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL K 435 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE K 468 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU K 437 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 458 through 459 Processing sheet with id=AD1, first strand: chain 'J' and resid 99 through 101 Processing sheet with id=AD2, first strand: chain 'J' and resid 99 through 101 removed outlier: 3.858A pdb=" N TYR J 9 " --> pdb=" O LYS J 189 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AD4, first strand: chain 'J' and resid 118 through 122 removed outlier: 6.737A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AD6, first strand: chain 'K' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'K' and resid 141 through 144 removed outlier: 6.627A pdb=" N GLU K 195 " --> pdb=" O SER K 167 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU K 192 " --> pdb=" O PHE K 394 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL K 396 " --> pdb=" O LEU K 192 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU K 194 " --> pdb=" O VAL K 396 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 445 through 447 Processing sheet with id=AD9, first strand: chain 'L' and resid 436 through 437 Processing sheet with id=AE1, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE2, first strand: chain 'P' and resid 105 through 106 Processing sheet with id=AE3, first strand: chain 'P' and resid 117 through 119 1037 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 9.86 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6779 1.33 - 1.46: 6825 1.46 - 1.59: 12182 1.59 - 1.72: 157 1.72 - 1.84: 168 Bond restraints: 26111 Sorted by residual: bond pdb=" C THR I 550 " pdb=" N GLN I 551 " ideal model delta sigma weight residual 1.334 1.449 -0.114 1.27e-02 6.20e+03 8.10e+01 bond pdb=" C ARG L 465 " pdb=" N ILE L 466 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.15e-02 7.56e+03 7.64e+01 bond pdb=" C ASP L 464 " pdb=" N ARG L 465 " ideal model delta sigma weight residual 1.331 1.449 -0.118 1.38e-02 5.25e+03 7.33e+01 bond pdb=" C SER P 76 " pdb=" N ARG P 77 " ideal model delta sigma weight residual 1.329 1.234 0.095 1.14e-02 7.69e+03 6.94e+01 bond pdb=" C ASP L 594 " pdb=" N LYS L 595 " ideal model delta sigma weight residual 1.334 1.428 -0.094 1.23e-02 6.61e+03 5.84e+01 ... (remaining 26106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 33953 2.75 - 5.49: 1444 5.49 - 8.24: 240 8.24 - 10.98: 22 10.98 - 13.73: 3 Bond angle restraints: 35662 Sorted by residual: angle pdb=" O THR I 550 " pdb=" C THR I 550 " pdb=" N GLN I 551 " ideal model delta sigma weight residual 122.12 129.50 -7.38 1.06e+00 8.90e-01 4.85e+01 angle pdb=" N GLY A 91 " pdb=" CA GLY A 91 " pdb=" C GLY A 91 " ideal model delta sigma weight residual 111.37 120.26 -8.89 1.29e+00 6.01e-01 4.75e+01 angle pdb=" CA THR I 550 " pdb=" C THR I 550 " pdb=" N GLN I 551 " ideal model delta sigma weight residual 117.30 109.90 7.40 1.16e+00 7.43e-01 4.07e+01 angle pdb=" O PHE G 56 " pdb=" C PHE G 56 " pdb=" N ASP G 57 " ideal model delta sigma weight residual 123.62 117.74 5.88 1.02e+00 9.61e-01 3.32e+01 angle pdb=" N ARG G 136 " pdb=" CA ARG G 136 " pdb=" C ARG G 136 " ideal model delta sigma weight residual 111.82 105.16 6.66 1.16e+00 7.43e-01 3.29e+01 ... (remaining 35657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 15342 34.90 - 69.80: 630 69.80 - 104.70: 46 104.70 - 139.60: 0 139.60 - 174.50: 2 Dihedral angle restraints: 16020 sinusoidal: 7242 harmonic: 8778 Sorted by residual: dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 46.50 -174.50 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C N -16 " pdb=" C1' C N -16 " pdb=" N1 C N -16 " pdb=" C2 C N -16 " ideal model delta sinusoidal sigma weight residual -128.00 45.44 -173.44 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA ALA H 314 " pdb=" C ALA H 314 " pdb=" N SER H 315 " pdb=" CA SER H 315 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 16017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 3891 0.135 - 0.271: 210 0.271 - 0.406: 11 0.406 - 0.542: 22 0.542 - 0.677: 1 Chirality restraints: 4135 Sorted by residual: chirality pdb=" CB ILE A 173 " pdb=" CA ILE A 173 " pdb=" CG1 ILE A 173 " pdb=" CG2 ILE A 173 " both_signs ideal model delta sigma weight residual False 2.64 1.97 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CB THR E 149 " pdb=" CA THR E 149 " pdb=" OG1 THR E 149 " pdb=" CG2 THR E 149 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" P G M 30 " pdb=" OP1 G M 30 " pdb=" OP2 G M 30 " pdb=" O5' G M 30 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 4132 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 79 " 0.802 9.50e-02 1.11e+02 3.60e-01 7.86e+01 pdb=" NE ARG C 79 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG C 79 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 79 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 79 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " 0.704 9.50e-02 1.11e+02 3.15e-01 6.07e+01 pdb=" NE ARG B 197 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 131 " 0.701 9.50e-02 1.11e+02 3.14e-01 6.03e+01 pdb=" NE ARG H 131 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG H 131 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 131 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 131 " 0.021 2.00e-02 2.50e+03 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 347 2.63 - 3.19: 22121 3.19 - 3.76: 41569 3.76 - 4.33: 57996 4.33 - 4.90: 93176 Nonbonded interactions: 215209 Sorted by model distance: nonbonded pdb=" O CYS P 81 " pdb="ZN ZN P 301 " model vdw 2.058 2.230 nonbonded pdb=" OG SER H 527 " pdb=" OP1 A N 5 " model vdw 2.228 3.040 nonbonded pdb=" OG SER K 527 " pdb=" OP1 U N 17 " model vdw 2.244 3.040 nonbonded pdb=" OG SER G 150 " pdb=" OP2 A M -4 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLU K 533 " pdb=" OH TYR K 548 " model vdw 2.317 3.040 ... (remaining 215204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or na \ me CA or name C or name O or name CB )) or resid 35 through 74 or (resid 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 78 or ( \ resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 th \ rough 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) o \ r resid 84 through 88 or (resid 89 and (name N or name CA or name C or name O or \ name CB )) or resid 90 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 110 or ( \ resid 111 through 112 and (name N or name CA or name C or name O or name CB )) o \ r resid 113 through 133 or (resid 134 and (name N or name CA or name C or name O \ or name CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or \ name C or name O or name CB )) or resid 138 through 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 or (resid 157 throug \ h 158 and (name N or name CA or name C or name O or name CB )) or resid 159 thro \ ugh 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) o \ r resid 171 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 301)) selection = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 32 or (resid 33 through 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 88 or (resid 89 and (name N or name CA or name C o \ r name O or name CB )) or resid 90 through 94 or (resid 95 through 96 and (name \ N or name CA or name C or name O or name CB )) or resid 97 through 107 or (resid \ 108 and (name N or name CA or name C or name O or name CB )) or resid 109 throu \ gh 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) or \ resid 113 through 133 or (resid 134 and (name N or name CA or name C or name O \ or name CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or n \ ame C or name O or name CB )) or resid 138 through 154 or (resid 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 or (resid 157 through \ 158 and (name N or name CA or name C or name O or name CB )) or resid 159 throu \ gh 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) or \ resid 171 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 301)) selection = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 32 or (resid 33 through 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 88 or (resid 89 and (name N or name CA or name C o \ r name O or name CB )) or resid 90 through 94 or (resid 95 through 96 and (name \ N or name CA or name C or name O or name CB )) or resid 97 through 107 or (resid \ 108 and (name N or name CA or name C or name O or name CB )) or resid 109 throu \ gh 110 or (resid 111 through 112 and (name N or name CA or name C or name O or n \ ame CB )) or resid 113 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 154 or (resid 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 or (resid \ 157 through 158 and (name N or name CA or name C or name O or name CB )) or res \ id 159 through 169 or (resid 170 and (name N or name CA or name C or name O or n \ ame CB )) or resid 171 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 32 or (resid 33 through 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 88 or (resid 89 and (name N or name CA or name C o \ r name O or name CB )) or resid 90 through 94 or (resid 95 through 96 and (name \ N or name CA or name C or name O or name CB )) or resid 97 through 110 or (resid \ 111 through 112 and (name N or name CA or name C or name O or name CB )) or res \ id 113 through 133 or (resid 134 and (name N or name CA or name C or name O or n \ ame CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 154 or (resid 155 and (name N or \ name CA or name C or name O or name CB )) or resid 156 or (resid 157 through 158 \ and (name N or name CA or name C or name O or name CB )) or resid 159 through 1 \ 69 or (resid 170 and (name N or name CA or name C or name O or name CB )) or res \ id 171 through 191 or (resid 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 196 or resid 301)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or na \ me CA or name C or name O or name CB )) or resid 35 through 74 or (resid 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 78 or ( \ resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 th \ rough 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) o \ r resid 84 through 88 or (resid 89 and (name N or name CA or name C or name O or \ name CB )) or resid 90 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 110 or ( \ resid 111 through 112 and (name N or name CA or name C or name O or name CB )) o \ r resid 113 through 133 or (resid 134 and (name N or name CA or name C or name O \ or name CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or \ name C or name O or name CB )) or resid 138 through 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 157 or (resi \ d 158 and (name N or name CA or name C or name O or name CB )) or resid 159 thro \ ugh 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) o \ r resid 171 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 301)) selection = (chain 'J' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 32 or (resid 33 through 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 74 or (re \ sid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 88 or (resid 89 and (name N or name CA or name C o \ r name O or name CB )) or resid 90 through 94 or (resid 95 through 96 and (name \ N or name CA or name C or name O or name CB )) or resid 97 through 107 or (resid \ 108 and (name N or name CA or name C or name O or name CB )) or resid 109 throu \ gh 110 or (resid 111 through 112 and (name N or name CA or name C or name O or n \ ame CB )) or resid 113 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 154 or (resid 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 or (resid \ 157 through 158 and (name N or name CA or name C or name O or name CB )) or res \ id 159 through 169 or (resid 170 and (name N or name CA or name C or name O or n \ ame CB )) or resid 171 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'P' and (resid 3 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 107 or (resid 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 110 or (resid 111 t \ hrough 112 and (name N or name CA or name C or name O or name CB )) or resid 113 \ through 195 or (resid 196 and (name N or name CA or name C or name O or name CB \ )) or resid 301)) } ncs_group { reference = (chain 'I' and ((resid 434 and (name N or name CA or name C or name O or name CB \ )) or resid 435 through 460 or (resid 461 and (name N or name CA or name C or n \ ame O or name CB )) or resid 462 or (resid 463 through 465 and (name N or name C \ A or name C or name O or name CB )) or resid 466 through 488 or resid 506 throug \ h 507 or (resid 508 and (name N or name CA or name C or name O or name CB )) or \ resid 509 through 510 or (resid 511 and (name N or name CA or name C or name O o \ r name CB )) or resid 512 through 514 or (resid 515 and (name N or name CA or na \ me C or name O or name CB )) or resid 516 through 517 or (resid 518 and (name N \ or name CA or name C or name O or name CB )) or resid 519 through 569 or (resid \ 570 and (name N or name CA or name C or name O or name CB )) or resid 571 throug \ h 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 through 607)) selection = (chain 'L' and (resid 434 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )) or resid 437 through 464 or (resid 465 and (name N \ or name CA or name C or name O or name CB )) or resid 466 through 542 or (resid \ 543 through 545 and (name N or name CA or name C or name O or name CB )) or resi \ d 546 through 607)) } 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.420 Check model and map are aligned: 0.290 Set scattering table: 0.330 Process input model: 73.750 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.009 0.363 26144 Z= 0.534 Angle : 1.338 28.858 35704 Z= 0.764 Chirality : 0.076 0.677 4135 Planarity : 0.017 0.360 4208 Dihedral : 17.283 174.504 10328 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.03 % Allowed : 20.28 % Favored : 77.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.13), residues: 2964 helix: -0.66 (0.14), residues: 976 sheet: -2.13 (0.21), residues: 540 loop : -2.12 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.005 TRP L 478 HIS 0.028 0.003 HIS L 553 PHE 0.062 0.005 PHE G 14 TYR 0.050 0.004 TYR H 245 ARG 0.028 0.002 ARG L 486 Details of bonding type rmsd hydrogen bonds : bond 0.15920 ( 1064) hydrogen bonds : angle 7.67319 ( 3100) metal coordination : bond 0.06471 ( 33) metal coordination : angle 12.47344 ( 42) covalent geometry : bond 0.00904 (26111) covalent geometry : angle 1.26813 (35662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 503 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 CYS cc_start: 0.7393 (m) cc_final: 0.6655 (m) REVERT: A 144 PHE cc_start: 0.8003 (m-10) cc_final: 0.7760 (m-10) REVERT: A 147 THR cc_start: 0.8568 (m) cc_final: 0.8082 (t) REVERT: A 167 PHE cc_start: 0.8316 (t80) cc_final: 0.8032 (t80) REVERT: A 185 SER cc_start: 0.7291 (t) cc_final: 0.7061 (p) REVERT: B 152 ASN cc_start: 0.8570 (p0) cc_final: 0.7930 (p0) REVERT: D 72 ASP cc_start: 0.8346 (p0) cc_final: 0.7998 (p0) REVERT: F 3 LYS cc_start: 0.6628 (mttt) cc_final: 0.6162 (pptt) REVERT: F 191 GLU cc_start: 0.8075 (tt0) cc_final: 0.7698 (tt0) REVERT: G 5 LYS cc_start: 0.4847 (OUTLIER) cc_final: 0.4246 (pttp) REVERT: H 136 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6489 (mp) REVERT: H 211 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8503 (tt) REVERT: H 603 ILE cc_start: 0.9032 (pp) cc_final: 0.8760 (pt) REVERT: I 438 ASN cc_start: 0.7789 (t0) cc_final: 0.7062 (t0) REVERT: I 551 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7954 (tp40) REVERT: I 568 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7636 (tp30) REVERT: K 473 TRP cc_start: 0.7617 (OUTLIER) cc_final: 0.7079 (t-100) REVERT: K 485 MET cc_start: 0.9083 (mmm) cc_final: 0.8233 (mmm) REVERT: K 584 TYR cc_start: 0.8237 (t80) cc_final: 0.7950 (t80) REVERT: L 483 ASN cc_start: 0.8709 (m-40) cc_final: 0.8372 (m110) REVERT: L 547 LYS cc_start: 0.8579 (tttt) cc_final: 0.8249 (ttpt) REVERT: P 131 ASP cc_start: 0.8114 (p0) cc_final: 0.7446 (m-30) REVERT: P 191 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7117 (tm-30) outliers start: 50 outliers final: 17 residues processed: 525 average time/residue: 0.4386 time to fit residues: 343.5654 Evaluate side-chains 410 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 478 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain P residue 191 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 112 GLN E 107 ASN F 154 GLN F 178 ASN H 108 ASN H 203 HIS H 236 GLN J 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096575 restraints weight = 38534.309| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.23 r_work: 0.3095 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26144 Z= 0.219 Angle : 0.711 22.327 35704 Z= 0.348 Chirality : 0.044 0.307 4135 Planarity : 0.005 0.074 4208 Dihedral : 15.732 174.270 4799 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.37 % Allowed : 16.86 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 2964 helix: 0.59 (0.16), residues: 989 sheet: -1.93 (0.20), residues: 532 loop : -1.80 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 478 HIS 0.008 0.001 HIS L 510 PHE 0.025 0.002 PHE D 103 TYR 0.017 0.001 TYR K 548 ARG 0.007 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1064) hydrogen bonds : angle 5.48291 ( 3100) metal coordination : bond 0.01362 ( 33) metal coordination : angle 8.44292 ( 42) covalent geometry : bond 0.00495 (26111) covalent geometry : angle 0.64992 (35662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 400 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.8296 (m-10) cc_final: 0.7858 (m-10) REVERT: B 112 GLN cc_start: 0.8282 (mt0) cc_final: 0.8081 (mt0) REVERT: B 123 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 152 ASN cc_start: 0.8625 (p0) cc_final: 0.8143 (p0) REVERT: D 72 ASP cc_start: 0.8563 (p0) cc_final: 0.8211 (p0) REVERT: F 3 LYS cc_start: 0.6779 (mttt) cc_final: 0.6270 (pptt) REVERT: F 34 ARG cc_start: 0.9010 (ttm-80) cc_final: 0.8576 (mtm110) REVERT: F 191 GLU cc_start: 0.8630 (tt0) cc_final: 0.8347 (tt0) REVERT: G 5 LYS cc_start: 0.5038 (OUTLIER) cc_final: 0.4383 (pttp) REVERT: G 148 LYS cc_start: 0.7890 (mptt) cc_final: 0.7420 (mttp) REVERT: H 211 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8609 (tt) REVERT: I 438 ASN cc_start: 0.8029 (t0) cc_final: 0.7224 (t0) REVERT: K 485 MET cc_start: 0.9177 (mmm) cc_final: 0.8620 (mmt) REVERT: L 451 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6516 (mtp85) REVERT: L 473 TRP cc_start: 0.8551 (t60) cc_final: 0.8288 (t60) REVERT: L 483 ASN cc_start: 0.8692 (m-40) cc_final: 0.8322 (m-40) REVERT: L 547 LYS cc_start: 0.8715 (tttt) cc_final: 0.8448 (ttpt) REVERT: L 591 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7377 (mt) REVERT: L 599 TYR cc_start: 0.8399 (t80) cc_final: 0.8091 (t80) REVERT: P 112 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8617 (mt0) REVERT: P 131 ASP cc_start: 0.8269 (p0) cc_final: 0.7699 (m-30) outliers start: 83 outliers final: 45 residues processed: 452 average time/residue: 0.4043 time to fit residues: 283.6647 Evaluate side-chains 413 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 112 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 253 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN E 32 GLN E 171 ASN F 178 ASN H 269 ASN H 335 ASN J 107 ASN J 112 GLN J 178 ASN P 154 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098477 restraints weight = 38578.448| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.56 r_work: 0.2995 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 26144 Z= 0.301 Angle : 0.722 18.541 35704 Z= 0.351 Chirality : 0.045 0.260 4135 Planarity : 0.005 0.057 4208 Dihedral : 15.509 172.923 4779 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.23 % Allowed : 17.55 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2964 helix: 0.89 (0.16), residues: 993 sheet: -1.78 (0.20), residues: 560 loop : -1.67 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 125 HIS 0.006 0.002 HIS P 119 PHE 0.022 0.002 PHE E 167 TYR 0.018 0.002 TYR K 548 ARG 0.005 0.001 ARG H 451 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1064) hydrogen bonds : angle 5.19628 ( 3100) metal coordination : bond 0.01434 ( 33) metal coordination : angle 8.28270 ( 42) covalent geometry : bond 0.00688 (26111) covalent geometry : angle 0.66417 (35662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 381 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7889 (ttm) cc_final: 0.7651 (mtp) REVERT: B 22 GLU cc_start: 0.8018 (tp30) cc_final: 0.7777 (tp30) REVERT: B 112 GLN cc_start: 0.8257 (mt0) cc_final: 0.8014 (mt0) REVERT: B 123 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 72 ASP cc_start: 0.8474 (p0) cc_final: 0.8182 (p0) REVERT: D 152 ASN cc_start: 0.8577 (t0) cc_final: 0.8160 (t0) REVERT: E 3 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7941 (mttt) REVERT: F 3 LYS cc_start: 0.6768 (mttt) cc_final: 0.6261 (pptt) REVERT: F 34 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8482 (mtm110) REVERT: F 191 GLU cc_start: 0.8560 (tt0) cc_final: 0.8226 (tt0) REVERT: G 5 LYS cc_start: 0.4857 (mmmt) cc_final: 0.4020 (pttp) REVERT: G 148 LYS cc_start: 0.7840 (mptt) cc_final: 0.7547 (mttp) REVERT: H 211 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8572 (tt) REVERT: H 310 VAL cc_start: 0.8200 (t) cc_final: 0.7979 (t) REVERT: I 438 ASN cc_start: 0.8069 (t0) cc_final: 0.7268 (t0) REVERT: I 477 ILE cc_start: 0.7641 (mm) cc_final: 0.7091 (tp) REVERT: J 72 ASP cc_start: 0.8257 (t70) cc_final: 0.7942 (t70) REVERT: L 451 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6649 (mtp85) REVERT: L 478 TRP cc_start: 0.9080 (t-100) cc_final: 0.8642 (t-100) REVERT: L 483 ASN cc_start: 0.8794 (m-40) cc_final: 0.8381 (m110) REVERT: L 547 LYS cc_start: 0.8702 (tttt) cc_final: 0.8369 (ttpt) REVERT: L 591 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7357 (mt) REVERT: L 599 TYR cc_start: 0.8455 (t80) cc_final: 0.8176 (t80) REVERT: P 98 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6024 (mtm-85) REVERT: P 112 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: P 131 ASP cc_start: 0.8248 (p0) cc_final: 0.7550 (m-30) REVERT: P 144 PHE cc_start: 0.9224 (m-80) cc_final: 0.8856 (m-10) REVERT: P 183 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6481 (mpp-170) REVERT: P 191 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7441 (tm-30) outliers start: 104 outliers final: 64 residues processed: 450 average time/residue: 0.4568 time to fit residues: 319.4916 Evaluate side-chains 418 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 348 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 183 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 12 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN E 32 GLN F 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095959 restraints weight = 38477.436| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.23 r_work: 0.3093 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26144 Z= 0.144 Angle : 0.611 16.060 35704 Z= 0.299 Chirality : 0.042 0.280 4135 Planarity : 0.004 0.052 4208 Dihedral : 15.522 176.710 4775 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.33 % Allowed : 17.96 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 2964 helix: 1.21 (0.16), residues: 995 sheet: -1.56 (0.21), residues: 544 loop : -1.52 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 478 HIS 0.005 0.001 HIS B 119 PHE 0.018 0.002 PHE E 167 TYR 0.015 0.001 TYR K 584 ARG 0.007 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1064) hydrogen bonds : angle 4.84914 ( 3100) metal coordination : bond 0.00813 ( 33) metal coordination : angle 6.69143 ( 42) covalent geometry : bond 0.00318 (26111) covalent geometry : angle 0.56651 (35662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 389 time to evaluate : 3.680 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7956 (ttm) cc_final: 0.7679 (mtp) REVERT: A 116 GLU cc_start: 0.8892 (mp0) cc_final: 0.8668 (mp0) REVERT: A 144 PHE cc_start: 0.8284 (m-10) cc_final: 0.7864 (m-10) REVERT: B 9 TYR cc_start: 0.8439 (m-80) cc_final: 0.8154 (m-80) REVERT: B 22 GLU cc_start: 0.8260 (tp30) cc_final: 0.7948 (tp30) REVERT: B 116 GLU cc_start: 0.7663 (tt0) cc_final: 0.7118 (mp0) REVERT: B 117 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 123 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 154 GLN cc_start: 0.7411 (mp10) cc_final: 0.7026 (mp10) REVERT: C 156 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (ttpp) REVERT: D 72 ASP cc_start: 0.8613 (p0) cc_final: 0.8316 (p0) REVERT: D 152 ASN cc_start: 0.8667 (t0) cc_final: 0.8203 (t0) REVERT: F 3 LYS cc_start: 0.6645 (mttt) cc_final: 0.6148 (pptt) REVERT: F 34 ARG cc_start: 0.8921 (ttm-80) cc_final: 0.8586 (mtm110) REVERT: F 191 GLU cc_start: 0.8576 (tt0) cc_final: 0.8215 (tt0) REVERT: G 5 LYS cc_start: 0.4836 (mmmt) cc_final: 0.3960 (pttp) REVERT: G 108 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7623 (ttmm) REVERT: G 130 GLU cc_start: 0.5768 (tp30) cc_final: 0.5451 (tp30) REVERT: G 134 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7804 (pt) REVERT: G 148 LYS cc_start: 0.7876 (mptt) cc_final: 0.7513 (mttp) REVERT: H 44 ILE cc_start: 0.8461 (mp) cc_final: 0.8253 (mp) REVERT: H 78 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.7909 (mtt-85) REVERT: H 160 HIS cc_start: 0.8996 (t70) cc_final: 0.8787 (t70) REVERT: H 211 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8598 (tt) REVERT: H 526 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8878 (mp) REVERT: I 438 ASN cc_start: 0.8188 (t0) cc_final: 0.7434 (t0) REVERT: I 453 MET cc_start: 0.8213 (ttt) cc_final: 0.7945 (ttt) REVERT: I 477 ILE cc_start: 0.7706 (mm) cc_final: 0.7238 (tp) REVERT: I 551 GLN cc_start: 0.8571 (tt0) cc_final: 0.8323 (tm-30) REVERT: L 451 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6404 (mtp85) REVERT: L 467 GLU cc_start: 0.7258 (pm20) cc_final: 0.6905 (pm20) REVERT: L 483 ASN cc_start: 0.8810 (m-40) cc_final: 0.8377 (m110) REVERT: L 547 LYS cc_start: 0.8679 (tttt) cc_final: 0.8374 (ttpt) REVERT: L 591 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7191 (mt) REVERT: L 599 TYR cc_start: 0.8431 (t80) cc_final: 0.8178 (t80) REVERT: P 112 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: P 123 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7229 (mt-10) REVERT: P 131 ASP cc_start: 0.8402 (p0) cc_final: 0.7633 (m-30) REVERT: P 169 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8027 (mm-30) REVERT: P 183 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6390 (mpp-170) REVERT: P 191 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7436 (tm-30) outliers start: 82 outliers final: 52 residues processed: 437 average time/residue: 0.4467 time to fit residues: 303.1271 Evaluate side-chains 414 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 526 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 173 optimal weight: 0.0970 chunk 22 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 250 optimal weight: 0.2980 chunk 240 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN F 154 GLN F 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099169 restraints weight = 38408.356| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.20 r_work: 0.3129 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26144 Z= 0.114 Angle : 0.575 13.913 35704 Z= 0.282 Chirality : 0.041 0.299 4135 Planarity : 0.003 0.040 4208 Dihedral : 15.485 178.928 4775 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.62 % Allowed : 18.12 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2964 helix: 1.42 (0.16), residues: 1010 sheet: -1.44 (0.21), residues: 544 loop : -1.33 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 478 HIS 0.004 0.001 HIS L 553 PHE 0.021 0.001 PHE L 538 TYR 0.016 0.001 TYR G 38 ARG 0.006 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1064) hydrogen bonds : angle 4.57604 ( 3100) metal coordination : bond 0.00576 ( 33) metal coordination : angle 5.71093 ( 42) covalent geometry : bond 0.00245 (26111) covalent geometry : angle 0.54053 (35662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 401 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7927 (ttm) cc_final: 0.7702 (mtp) REVERT: A 93 MET cc_start: 0.8477 (tpp) cc_final: 0.8264 (mmm) REVERT: A 116 GLU cc_start: 0.8919 (mp0) cc_final: 0.8713 (mp0) REVERT: A 144 PHE cc_start: 0.8263 (m-10) cc_final: 0.7903 (m-10) REVERT: A 187 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7239 (mp0) REVERT: B 9 TYR cc_start: 0.8475 (m-80) cc_final: 0.8177 (m-80) REVERT: B 22 GLU cc_start: 0.8193 (tp30) cc_final: 0.7900 (tp30) REVERT: B 116 GLU cc_start: 0.7655 (tt0) cc_final: 0.7168 (mp0) REVERT: B 117 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8055 (p) REVERT: B 123 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7134 (tm-30) REVERT: C 25 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8215 (ttp-170) REVERT: C 156 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (ttpp) REVERT: D 72 ASP cc_start: 0.8612 (p0) cc_final: 0.8383 (p0) REVERT: D 111 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: D 152 ASN cc_start: 0.8704 (t0) cc_final: 0.8216 (t0) REVERT: E 150 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8839 (mm) REVERT: F 3 LYS cc_start: 0.6605 (mttt) cc_final: 0.6071 (pptt) REVERT: F 19 TYR cc_start: 0.9351 (t80) cc_final: 0.9090 (t80) REVERT: F 34 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8546 (mtm110) REVERT: G 5 LYS cc_start: 0.4924 (mmmt) cc_final: 0.4110 (pttp) REVERT: G 83 LEU cc_start: 0.7027 (mp) cc_final: 0.6725 (mm) REVERT: G 108 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7614 (ttmm) REVERT: G 130 GLU cc_start: 0.6108 (tp30) cc_final: 0.5776 (tp30) REVERT: G 148 LYS cc_start: 0.7872 (mptt) cc_final: 0.7551 (mttp) REVERT: H 78 ARG cc_start: 0.8740 (mtt-85) cc_final: 0.8039 (mtt-85) REVERT: H 91 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8087 (mp0) REVERT: H 103 ILE cc_start: 0.8631 (mm) cc_final: 0.8397 (mm) REVERT: H 158 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7781 (mt-10) REVERT: H 160 HIS cc_start: 0.8997 (t70) cc_final: 0.8699 (t70) REVERT: H 211 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8619 (tt) REVERT: H 526 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8823 (mp) REVERT: I 438 ASN cc_start: 0.8178 (t0) cc_final: 0.7485 (t0) REVERT: I 453 MET cc_start: 0.8278 (ttt) cc_final: 0.7946 (ttt) REVERT: I 477 ILE cc_start: 0.7761 (mm) cc_final: 0.7258 (tp) REVERT: I 485 MET cc_start: 0.6903 (mmt) cc_final: 0.6555 (mmp) REVERT: J 140 GLU cc_start: 0.8798 (mp0) cc_final: 0.8486 (mp0) REVERT: K 444 MET cc_start: 0.6822 (ttm) cc_final: 0.6528 (mtp) REVERT: L 451 ARG cc_start: 0.7092 (mtp180) cc_final: 0.6466 (mtp85) REVERT: L 465 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6038 (mtt180) REVERT: L 473 TRP cc_start: 0.8613 (t60) cc_final: 0.8316 (t60) REVERT: L 483 ASN cc_start: 0.8763 (m-40) cc_final: 0.8326 (m-40) REVERT: L 547 LYS cc_start: 0.8635 (tttt) cc_final: 0.8337 (ttpt) REVERT: L 577 GLU cc_start: 0.8809 (tp30) cc_final: 0.8566 (mm-30) REVERT: L 599 TYR cc_start: 0.8423 (t80) cc_final: 0.8167 (t80) REVERT: P 112 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: P 123 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7173 (mt-10) REVERT: P 169 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8076 (mm-30) REVERT: P 183 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6449 (mpp-170) REVERT: P 191 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7591 (tm-30) outliers start: 89 outliers final: 49 residues processed: 454 average time/residue: 0.4744 time to fit residues: 332.5731 Evaluate side-chains 427 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 368 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 526 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 450 TYR Chi-restraints excluded: chain I residue 476 MET Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 465 ARG Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 28 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN E 32 GLN F 154 GLN F 178 ASN H 62 HIS I 551 GLN J 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095682 restraints weight = 38213.036| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.22 r_work: 0.3089 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26144 Z= 0.169 Angle : 0.602 14.389 35704 Z= 0.295 Chirality : 0.042 0.271 4135 Planarity : 0.003 0.040 4208 Dihedral : 15.415 177.145 4772 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.74 % Allowed : 18.94 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2964 helix: 1.47 (0.16), residues: 1011 sheet: -1.42 (0.21), residues: 554 loop : -1.23 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 478 HIS 0.004 0.001 HIS B 119 PHE 0.018 0.002 PHE K 122 TYR 0.013 0.001 TYR G 161 ARG 0.005 0.000 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1064) hydrogen bonds : angle 4.56020 ( 3100) metal coordination : bond 0.00794 ( 33) metal coordination : angle 6.06575 ( 42) covalent geometry : bond 0.00382 (26111) covalent geometry : angle 0.56493 (35662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 380 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8097 (mtt90) REVERT: A 144 PHE cc_start: 0.8302 (m-10) cc_final: 0.7912 (m-10) REVERT: A 187 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7187 (mp0) REVERT: B 22 GLU cc_start: 0.8227 (tp30) cc_final: 0.7934 (tp30) REVERT: B 116 GLU cc_start: 0.7658 (tt0) cc_final: 0.7237 (mp0) REVERT: B 117 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 123 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7080 (tm-30) REVERT: C 156 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7724 (ttpp) REVERT: D 72 ASP cc_start: 0.8687 (p0) cc_final: 0.8442 (p0) REVERT: D 152 ASN cc_start: 0.8712 (t0) cc_final: 0.8214 (t0) REVERT: E 150 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8868 (mm) REVERT: F 3 LYS cc_start: 0.6622 (mttt) cc_final: 0.6127 (pptt) REVERT: G 5 LYS cc_start: 0.4988 (mmmt) cc_final: 0.4230 (pttp) REVERT: G 83 LEU cc_start: 0.7052 (mp) cc_final: 0.6753 (mm) REVERT: G 108 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7617 (ttmm) REVERT: G 148 LYS cc_start: 0.7889 (mptt) cc_final: 0.7532 (mttp) REVERT: H 78 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.8011 (mtt-85) REVERT: H 91 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8133 (mp0) REVERT: H 103 ILE cc_start: 0.8606 (mm) cc_final: 0.8354 (mm) REVERT: H 211 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8602 (tt) REVERT: H 594 ASP cc_start: 0.7913 (m-30) cc_final: 0.7509 (p0) REVERT: I 438 ASN cc_start: 0.8181 (t0) cc_final: 0.7533 (t0) REVERT: I 455 PHE cc_start: 0.8337 (t80) cc_final: 0.8122 (t80) REVERT: I 477 ILE cc_start: 0.7755 (mm) cc_final: 0.7253 (tp) REVERT: I 485 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6621 (mmp) REVERT: K 116 ASP cc_start: 0.7298 (m-30) cc_final: 0.6894 (p0) REVERT: L 451 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6600 (mtp85) REVERT: L 465 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5980 (mtp85) REVERT: L 483 ASN cc_start: 0.8768 (m-40) cc_final: 0.8320 (m110) REVERT: L 547 LYS cc_start: 0.8596 (tttt) cc_final: 0.8291 (ttpt) REVERT: L 577 GLU cc_start: 0.8840 (tp30) cc_final: 0.8617 (mm-30) REVERT: L 599 TYR cc_start: 0.8409 (t80) cc_final: 0.8200 (t80) REVERT: P 98 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5937 (mtm-85) REVERT: P 112 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: P 131 ASP cc_start: 0.8115 (p0) cc_final: 0.7326 (m-30) REVERT: P 169 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8079 (mm-30) REVERT: P 183 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.6549 (mpp-170) REVERT: P 191 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7600 (tm-30) outliers start: 92 outliers final: 63 residues processed: 431 average time/residue: 0.3861 time to fit residues: 256.7862 Evaluate side-chains 435 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 476 MET Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 465 ARG Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 119 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 99 optimal weight: 0.0470 chunk 171 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN E 32 GLN F 154 GLN F 178 ASN J 107 ASN J 112 GLN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094466 restraints weight = 38424.064| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.22 r_work: 0.3071 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26144 Z= 0.203 Angle : 0.620 14.786 35704 Z= 0.303 Chirality : 0.043 0.269 4135 Planarity : 0.004 0.040 4208 Dihedral : 15.362 176.215 4770 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.94 % Allowed : 19.26 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2964 helix: 1.51 (0.16), residues: 1006 sheet: -1.36 (0.21), residues: 559 loop : -1.22 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 478 HIS 0.004 0.001 HIS B 119 PHE 0.019 0.002 PHE L 447 TYR 0.014 0.001 TYR H 245 ARG 0.008 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1064) hydrogen bonds : angle 4.55814 ( 3100) metal coordination : bond 0.00932 ( 33) metal coordination : angle 6.31302 ( 42) covalent geometry : bond 0.00463 (26111) covalent geometry : angle 0.58164 (35662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 378 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8160 (mtt90) REVERT: A 144 PHE cc_start: 0.8297 (m-10) cc_final: 0.7918 (m-10) REVERT: A 187 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7110 (mp0) REVERT: B 22 GLU cc_start: 0.8232 (tp30) cc_final: 0.7937 (tp30) REVERT: B 116 GLU cc_start: 0.7652 (tt0) cc_final: 0.7220 (mp0) REVERT: B 117 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 123 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 72 ASP cc_start: 0.8630 (p0) cc_final: 0.8374 (p0) REVERT: D 152 ASN cc_start: 0.8733 (t0) cc_final: 0.8189 (t0) REVERT: E 3 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8005 (mttt) REVERT: E 150 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8857 (mm) REVERT: F 3 LYS cc_start: 0.6653 (mttt) cc_final: 0.6121 (pptt) REVERT: G 5 LYS cc_start: 0.4967 (mmmt) cc_final: 0.4197 (pttp) REVERT: G 83 LEU cc_start: 0.7120 (mp) cc_final: 0.6815 (mm) REVERT: G 96 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7523 (p) REVERT: G 108 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7588 (ttmm) REVERT: G 148 LYS cc_start: 0.7831 (mptt) cc_final: 0.7528 (mttp) REVERT: H 78 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8005 (mtt-85) REVERT: H 103 ILE cc_start: 0.8572 (mm) cc_final: 0.8323 (mm) REVERT: H 158 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 211 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8685 (tt) REVERT: H 537 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8232 (mm-30) REVERT: I 438 ASN cc_start: 0.8293 (t0) cc_final: 0.7639 (t0) REVERT: I 455 PHE cc_start: 0.8436 (t80) cc_final: 0.8123 (t80) REVERT: J 72 ASP cc_start: 0.8423 (t70) cc_final: 0.8137 (t70) REVERT: K 116 ASP cc_start: 0.7233 (m-30) cc_final: 0.6848 (p0) REVERT: L 451 ARG cc_start: 0.7328 (mtp180) cc_final: 0.6708 (mtp85) REVERT: L 465 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6018 (mtp85) REVERT: L 478 TRP cc_start: 0.8703 (t-100) cc_final: 0.8198 (t-100) REVERT: L 483 ASN cc_start: 0.8796 (m-40) cc_final: 0.8348 (m110) REVERT: L 547 LYS cc_start: 0.8578 (tttt) cc_final: 0.8253 (ttpt) REVERT: P 98 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5991 (mtm-85) REVERT: P 112 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: P 123 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7278 (mt-10) REVERT: P 131 ASP cc_start: 0.8097 (p0) cc_final: 0.7307 (m-30) REVERT: P 183 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.6444 (mpp-170) REVERT: P 191 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7548 (tm-30) outliers start: 97 outliers final: 67 residues processed: 435 average time/residue: 0.3997 time to fit residues: 267.8981 Evaluate side-chains 437 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 359 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 476 MET Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 450 TYR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 465 ARG Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 74 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN E 32 GLN J 112 GLN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094249 restraints weight = 38362.097| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.15 r_work: 0.3069 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26144 Z= 0.212 Angle : 0.627 14.737 35704 Z= 0.308 Chirality : 0.043 0.294 4135 Planarity : 0.004 0.040 4208 Dihedral : 15.334 175.982 4767 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.62 % Allowed : 19.59 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2964 helix: 1.48 (0.16), residues: 1006 sheet: -1.32 (0.21), residues: 554 loop : -1.21 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 478 HIS 0.005 0.001 HIS B 119 PHE 0.020 0.002 PHE L 447 TYR 0.015 0.001 TYR J 181 ARG 0.008 0.001 ARG H 361 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 1064) hydrogen bonds : angle 4.55948 ( 3100) metal coordination : bond 0.00971 ( 33) metal coordination : angle 6.36344 ( 42) covalent geometry : bond 0.00481 (26111) covalent geometry : angle 0.58845 (35662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 378 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7947 (ttm) cc_final: 0.7714 (mtp) REVERT: A 77 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8162 (mtt90) REVERT: A 144 PHE cc_start: 0.8307 (m-10) cc_final: 0.7890 (m-10) REVERT: A 187 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7193 (mp0) REVERT: B 9 TYR cc_start: 0.8632 (m-80) cc_final: 0.8414 (m-80) REVERT: B 22 GLU cc_start: 0.8234 (tp30) cc_final: 0.7939 (tp30) REVERT: B 116 GLU cc_start: 0.7701 (tt0) cc_final: 0.7190 (mp0) REVERT: B 123 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7049 (tm-30) REVERT: C 25 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8186 (ttp80) REVERT: D 72 ASP cc_start: 0.8632 (p0) cc_final: 0.8364 (p0) REVERT: D 152 ASN cc_start: 0.8704 (t0) cc_final: 0.8124 (t0) REVERT: E 3 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (mttt) REVERT: E 131 ASP cc_start: 0.8834 (m-30) cc_final: 0.8605 (t0) REVERT: E 150 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8855 (mm) REVERT: F 3 LYS cc_start: 0.6641 (mttt) cc_final: 0.6113 (pptt) REVERT: G 5 LYS cc_start: 0.4939 (mmmt) cc_final: 0.4198 (pttp) REVERT: G 83 LEU cc_start: 0.7166 (mp) cc_final: 0.6880 (mm) REVERT: G 108 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7561 (ttmm) REVERT: G 134 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8050 (pt) REVERT: G 148 LYS cc_start: 0.7788 (mptt) cc_final: 0.7501 (mttp) REVERT: H 1 MET cc_start: 0.7282 (pmm) cc_final: 0.6910 (pmm) REVERT: H 103 ILE cc_start: 0.8552 (mm) cc_final: 0.8258 (mm) REVERT: H 158 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7860 (mt-10) REVERT: H 537 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8192 (mm-30) REVERT: I 438 ASN cc_start: 0.8293 (t0) cc_final: 0.7651 (t0) REVERT: I 453 MET cc_start: 0.8315 (ttt) cc_final: 0.7983 (ttt) REVERT: I 455 PHE cc_start: 0.8421 (t80) cc_final: 0.8104 (t80) REVERT: J 72 ASP cc_start: 0.8460 (t70) cc_final: 0.8160 (t70) REVERT: K 116 ASP cc_start: 0.7259 (m-30) cc_final: 0.6881 (p0) REVERT: K 145 ASN cc_start: 0.8082 (p0) cc_final: 0.7846 (p0) REVERT: L 451 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6716 (mtp85) REVERT: L 478 TRP cc_start: 0.8763 (t-100) cc_final: 0.8267 (t-100) REVERT: L 483 ASN cc_start: 0.8811 (m-40) cc_final: 0.8363 (m110) REVERT: L 547 LYS cc_start: 0.8558 (tttt) cc_final: 0.8227 (ttpt) REVERT: P 98 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5980 (mtm-85) REVERT: P 112 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: P 131 ASP cc_start: 0.8097 (p0) cc_final: 0.7311 (m-30) REVERT: P 169 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8229 (mm-30) REVERT: P 183 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.6434 (mpp-170) outliers start: 89 outliers final: 66 residues processed: 432 average time/residue: 0.3901 time to fit residues: 261.2115 Evaluate side-chains 436 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 362 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 464 ASP Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 284 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 0.0770 chunk 137 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN J 107 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095866 restraints weight = 38444.075| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.23 r_work: 0.3081 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26144 Z= 0.155 Angle : 0.600 14.135 35704 Z= 0.295 Chirality : 0.042 0.295 4135 Planarity : 0.003 0.039 4208 Dihedral : 15.308 177.500 4765 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.29 % Allowed : 20.15 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2964 helix: 1.54 (0.16), residues: 1011 sheet: -1.27 (0.21), residues: 555 loop : -1.16 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 478 HIS 0.006 0.001 HIS B 119 PHE 0.019 0.001 PHE L 447 TYR 0.014 0.001 TYR H 245 ARG 0.009 0.000 ARG H 361 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1064) hydrogen bonds : angle 4.48072 ( 3100) metal coordination : bond 0.00717 ( 33) metal coordination : angle 5.86031 ( 42) covalent geometry : bond 0.00350 (26111) covalent geometry : angle 0.56616 (35662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8097 (ttm) cc_final: 0.7891 (mtp) REVERT: A 77 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8242 (mtt90) REVERT: A 87 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6981 (m) REVERT: A 93 MET cc_start: 0.8425 (tpp) cc_final: 0.8208 (mmm) REVERT: A 144 PHE cc_start: 0.8350 (m-10) cc_final: 0.7985 (m-10) REVERT: A 187 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7251 (mp0) REVERT: B 9 TYR cc_start: 0.8657 (m-80) cc_final: 0.8454 (m-80) REVERT: B 22 GLU cc_start: 0.8235 (tp30) cc_final: 0.7927 (tp30) REVERT: B 25 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7324 (tmm-80) REVERT: B 116 GLU cc_start: 0.7655 (tt0) cc_final: 0.7242 (mp0) REVERT: B 123 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 25 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8243 (ttp80) REVERT: C 93 MET cc_start: 0.8220 (tpp) cc_final: 0.7621 (tpt) REVERT: D 72 ASP cc_start: 0.8637 (p0) cc_final: 0.8387 (p0) REVERT: D 152 ASN cc_start: 0.8737 (t0) cc_final: 0.8197 (t0) REVERT: E 150 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8887 (mm) REVERT: F 3 LYS cc_start: 0.6639 (mttt) cc_final: 0.6165 (pptt) REVERT: G 5 LYS cc_start: 0.5043 (mmmt) cc_final: 0.4260 (pttp) REVERT: G 83 LEU cc_start: 0.7211 (mp) cc_final: 0.6928 (mm) REVERT: G 108 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7650 (ttmm) REVERT: G 134 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8119 (pt) REVERT: G 148 LYS cc_start: 0.7843 (mptt) cc_final: 0.7543 (mttp) REVERT: H 1 MET cc_start: 0.7452 (pmm) cc_final: 0.7180 (pmm) REVERT: H 103 ILE cc_start: 0.8579 (mm) cc_final: 0.8294 (mm) REVERT: H 158 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7848 (mt-10) REVERT: H 594 ASP cc_start: 0.7906 (m-30) cc_final: 0.7451 (p0) REVERT: I 438 ASN cc_start: 0.8249 (t0) cc_final: 0.7645 (t0) REVERT: I 455 PHE cc_start: 0.8434 (t80) cc_final: 0.8092 (t80) REVERT: I 485 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6656 (mmp) REVERT: J 72 ASP cc_start: 0.8416 (t70) cc_final: 0.8142 (t70) REVERT: J 196 ASP cc_start: 0.8616 (p0) cc_final: 0.8390 (p0) REVERT: K 116 ASP cc_start: 0.7229 (m-30) cc_final: 0.6881 (p0) REVERT: K 145 ASN cc_start: 0.8066 (p0) cc_final: 0.7829 (p0) REVERT: L 451 ARG cc_start: 0.7369 (mtp180) cc_final: 0.6758 (mtp85) REVERT: L 473 TRP cc_start: 0.8735 (t60) cc_final: 0.8448 (t60) REVERT: L 483 ASN cc_start: 0.8784 (m-40) cc_final: 0.8351 (m-40) REVERT: L 547 LYS cc_start: 0.8625 (tttt) cc_final: 0.8292 (ttpt) REVERT: L 577 GLU cc_start: 0.8845 (tp30) cc_final: 0.8632 (mm-30) REVERT: P 98 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6040 (mtm-85) REVERT: P 112 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: P 131 ASP cc_start: 0.8060 (p0) cc_final: 0.7274 (m-30) REVERT: P 169 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8294 (mm-30) REVERT: P 183 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6472 (mpp-170) REVERT: P 191 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7789 (tm-30) outliers start: 81 outliers final: 63 residues processed: 425 average time/residue: 0.5466 time to fit residues: 365.6946 Evaluate side-chains 441 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 368 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 604 ASN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 283 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 292 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 438 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 = 0.3791 r_free = 0.3791 target = 0.138567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094809 restraints weight = 38217.902| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.22 r_work: 0.3065 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26144 Z= 0.188 Angle : 0.622 14.337 35704 Z= 0.305 Chirality : 0.042 0.291 4135 Planarity : 0.003 0.040 4208 Dihedral : 15.246 176.533 4765 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.09 % Allowed : 20.36 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2964 helix: 1.57 (0.16), residues: 1006 sheet: -1.19 (0.21), residues: 553 loop : -1.17 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 478 HIS 0.006 0.001 HIS B 119 PHE 0.020 0.002 PHE L 447 TYR 0.015 0.001 TYR H 245 ARG 0.010 0.000 ARG H 361 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1064) hydrogen bonds : angle 4.48758 ( 3100) metal coordination : bond 0.00869 ( 33) metal coordination : angle 6.06614 ( 42) covalent geometry : bond 0.00429 (26111) covalent geometry : angle 0.58684 (35662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 2.765 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8261 (mtt90) REVERT: A 87 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6979 (m) REVERT: A 93 MET cc_start: 0.8426 (tpp) cc_final: 0.8203 (mmm) REVERT: A 144 PHE cc_start: 0.8390 (m-10) cc_final: 0.8010 (m-10) REVERT: A 187 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7232 (mp0) REVERT: B 25 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7357 (tmm-80) REVERT: B 116 GLU cc_start: 0.7653 (tt0) cc_final: 0.7118 (mp0) REVERT: B 123 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 25 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8242 (ttp80) REVERT: C 93 MET cc_start: 0.8376 (tpp) cc_final: 0.7641 (tpt) REVERT: D 72 ASP cc_start: 0.8630 (p0) cc_final: 0.8387 (p0) REVERT: D 152 ASN cc_start: 0.8784 (t0) cc_final: 0.8240 (t0) REVERT: E 150 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8905 (mm) REVERT: F 3 LYS cc_start: 0.6660 (mttt) cc_final: 0.6168 (pptt) REVERT: G 5 LYS cc_start: 0.5068 (mmmt) cc_final: 0.4304 (pttp) REVERT: G 75 TYR cc_start: 0.7945 (m-10) cc_final: 0.7602 (m-80) REVERT: G 83 LEU cc_start: 0.7184 (mp) cc_final: 0.6901 (mm) REVERT: G 108 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7623 (ttmm) REVERT: G 148 LYS cc_start: 0.7831 (mptt) cc_final: 0.7534 (mttp) REVERT: H 1 MET cc_start: 0.7361 (pmm) cc_final: 0.7130 (pmm) REVERT: H 103 ILE cc_start: 0.8578 (mm) cc_final: 0.8291 (mm) REVERT: H 158 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7840 (mt-10) REVERT: H 594 ASP cc_start: 0.7912 (m-30) cc_final: 0.7461 (p0) REVERT: I 438 ASN cc_start: 0.8225 (t0) cc_final: 0.7654 (t0) REVERT: I 455 PHE cc_start: 0.8411 (t80) cc_final: 0.8134 (t80) REVERT: I 485 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6582 (mmp) REVERT: J 72 ASP cc_start: 0.8385 (t70) cc_final: 0.8158 (t70) REVERT: J 196 ASP cc_start: 0.8629 (p0) cc_final: 0.8397 (p0) REVERT: K 116 ASP cc_start: 0.7234 (m-30) cc_final: 0.6867 (p0) REVERT: K 145 ASN cc_start: 0.8067 (p0) cc_final: 0.7833 (p0) REVERT: L 451 ARG cc_start: 0.7376 (mtp180) cc_final: 0.6754 (mtp85) REVERT: L 465 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5448 (mtt180) REVERT: L 478 TRP cc_start: 0.8644 (t-100) cc_final: 0.8103 (t-100) REVERT: L 483 ASN cc_start: 0.8773 (m-40) cc_final: 0.8328 (m110) REVERT: L 485 MET cc_start: 0.7556 (mmm) cc_final: 0.7217 (mmm) REVERT: L 533 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7950 (mt-10) REVERT: L 547 LYS cc_start: 0.8608 (tttt) cc_final: 0.8277 (ttpt) REVERT: P 98 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6030 (mtm-85) REVERT: P 112 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: P 131 ASP cc_start: 0.8058 (p0) cc_final: 0.7280 (m-30) REVERT: P 169 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8295 (mm-30) REVERT: P 183 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6451 (mpp-170) REVERT: P 191 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7796 (tm-30) outliers start: 76 outliers final: 60 residues processed: 418 average time/residue: 0.3926 time to fit residues: 253.7419 Evaluate side-chains 433 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 363 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 219 CYS Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 604 ASN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 465 ARG Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 92 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 262 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 284 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN H 101 GLN J 107 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095048 restraints weight = 38330.141| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.19 r_work: 0.3076 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26144 Z= 0.180 Angle : 0.613 14.242 35704 Z= 0.301 Chirality : 0.042 0.293 4135 Planarity : 0.003 0.039 4208 Dihedral : 15.230 176.815 4765 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.37 % Allowed : 20.28 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2964 helix: 1.59 (0.16), residues: 1007 sheet: -1.14 (0.21), residues: 553 loop : -1.16 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 478 HIS 0.007 0.001 HIS B 119 PHE 0.020 0.002 PHE L 447 TYR 0.023 0.001 TYR G 38 ARG 0.010 0.000 ARG H 361 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1064) hydrogen bonds : angle 4.45324 ( 3100) metal coordination : bond 0.00829 ( 33) metal coordination : angle 5.95894 ( 42) covalent geometry : bond 0.00411 (26111) covalent geometry : angle 0.57821 (35662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15371.15 seconds wall clock time: 272 minutes 14.21 seconds (16334.21 seconds total)