Starting phenix.real_space_refine on Mon Aug 25 04:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z99_39857/08_2025/8z99_39857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z99_39857/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z99_39857/08_2025/8z99_39857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z99_39857/08_2025/8z99_39857_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z99_39857/08_2025/8z99_39857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z99_39857/08_2025/8z99_39857.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 11, 'ASP:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 5, 'TYR: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, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 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: {'GLU:plan': 13, 'ASP:plan': 6, 'HIS:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 1} 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: 6.09, per 1000 atoms: 0.24 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: 1.99 Conformation dependent library (CDL) restraints added in 762.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 3.09 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: 4.53 Time building geometry restraints manager: 2.47 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: 1.910 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.080 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- 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 : 7.10 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.028 0.002 ARG L 486 TYR 0.050 0.004 TYR H 245 PHE 0.062 0.005 PHE G 14 TRP 0.096 0.005 TRP L 478 HIS 0.028 0.003 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00904 (26111) covalent geometry : angle 1.26813 (35662) hydrogen bonds : bond 0.15920 ( 1064) hydrogen bonds : angle 7.67319 ( 3100) metal coordination : bond 0.06471 ( 33) metal coordination : angle 12.47344 ( 42) *********************** 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 : 0.823 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: 0.1973 time to fit residues: 155.3870 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 : 0.843 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 236 GLN J 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099874 restraints weight = 38533.824| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.23 r_work: 0.3146 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26144 Z= 0.158 Angle : 0.684 23.346 35704 Z= 0.335 Chirality : 0.043 0.310 4135 Planarity : 0.005 0.073 4208 Dihedral : 15.799 175.179 4799 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.01 % Allowed : 16.86 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 2964 helix: 0.59 (0.16), residues: 1001 sheet: -1.86 (0.20), residues: 535 loop : -1.82 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.014 0.001 TYR H 245 PHE 0.023 0.002 PHE K 166 TRP 0.032 0.002 TRP L 478 HIS 0.005 0.001 HIS L 510 Details of bonding type rmsd covalent geometry : bond 0.00347 (26111) covalent geometry : angle 0.62341 (35662) hydrogen bonds : bond 0.04589 ( 1064) hydrogen bonds : angle 5.48731 ( 3100) metal coordination : bond 0.01016 ( 33) metal coordination : angle 8.24116 ( 42) *********************** 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: 74 poor density : 409 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 144 PHE cc_start: 0.8219 (m-10) cc_final: 0.7851 (m-10) REVERT: B 112 GLN cc_start: 0.8245 (mt0) cc_final: 0.8028 (mt0) REVERT: B 152 ASN cc_start: 0.8589 (p0) cc_final: 0.8152 (p0) REVERT: B 196 ASP cc_start: 0.8841 (p0) cc_final: 0.8639 (p0) REVERT: D 72 ASP cc_start: 0.8527 (p0) cc_final: 0.8167 (p0) REVERT: D 111 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: D 112 GLN cc_start: 0.9116 (mt0) cc_final: 0.8853 (mt0) REVERT: F 3 LYS cc_start: 0.6732 (mttt) cc_final: 0.6204 (pptt) REVERT: F 34 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8575 (mtm110) REVERT: F 191 GLU cc_start: 0.8539 (tt0) cc_final: 0.8250 (tt0) REVERT: G 5 LYS cc_start: 0.4873 (OUTLIER) cc_final: 0.4168 (pttp) REVERT: G 148 LYS cc_start: 0.7874 (mptt) cc_final: 0.7407 (mttp) REVERT: H 62 HIS cc_start: 0.8577 (p-80) cc_final: 0.8168 (p90) REVERT: H 211 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8610 (tt) REVERT: I 438 ASN cc_start: 0.7996 (t0) cc_final: 0.7195 (t0) REVERT: J 155 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7309 (tm-30) REVERT: K 468 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7229 (mm) REVERT: K 485 MET cc_start: 0.9139 (mmm) cc_final: 0.8573 (mmt) REVERT: K 584 TYR cc_start: 0.8545 (t80) cc_final: 0.8164 (t80) REVERT: L 451 ARG cc_start: 0.6853 (mtp180) cc_final: 0.6615 (mtp85) REVERT: L 483 ASN cc_start: 0.8682 (m-40) cc_final: 0.8318 (m-40) REVERT: L 547 LYS cc_start: 0.8698 (tttt) cc_final: 0.8428 (ttpt) REVERT: L 591 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7401 (mt) REVERT: L 599 TYR cc_start: 0.8377 (t80) cc_final: 0.7980 (t80) REVERT: P 112 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: P 131 ASP cc_start: 0.8266 (p0) cc_final: 0.7640 (m-30) REVERT: P 144 PHE cc_start: 0.9258 (m-80) cc_final: 0.8775 (m-10) outliers start: 74 outliers final: 39 residues processed: 452 average time/residue: 0.1923 time to fit residues: 135.1488 Evaluate side-chains 411 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 365 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 C residue 177 LEU 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 E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 188 VAL 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 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 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 K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 468 ILE 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 554 ARG 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 273 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 203 HIS H 269 ASN J 112 GLN J 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095281 restraints weight = 38738.733| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.21 r_work: 0.3072 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26144 Z= 0.237 Angle : 0.671 17.363 35704 Z= 0.327 Chirality : 0.044 0.265 4135 Planarity : 0.005 0.058 4208 Dihedral : 15.511 174.044 4779 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.66 % Allowed : 17.55 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 2964 helix: 1.02 (0.16), residues: 995 sheet: -1.69 (0.20), residues: 560 loop : -1.62 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 197 TYR 0.016 0.001 TYR K 548 PHE 0.022 0.002 PHE D 103 TRP 0.032 0.002 TRP K 125 HIS 0.004 0.001 HIS P 119 Details of bonding type rmsd covalent geometry : bond 0.00532 (26111) covalent geometry : angle 0.61683 (35662) hydrogen bonds : bond 0.04176 ( 1064) hydrogen bonds : angle 5.05448 ( 3100) metal coordination : bond 0.01176 ( 33) metal coordination : angle 7.69401 ( 42) *********************** 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 477 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7925 (ttm) cc_final: 0.7688 (mtp) REVERT: A 144 PHE cc_start: 0.8314 (m-10) cc_final: 0.7882 (m-10) REVERT: A 187 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 22 GLU cc_start: 0.8172 (tp30) cc_final: 0.7819 (tp30) REVERT: B 112 GLN cc_start: 0.8314 (mt0) cc_final: 0.8095 (mt0) REVERT: B 123 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 72 ASP cc_start: 0.8600 (p0) cc_final: 0.8312 (p0) REVERT: D 152 ASN cc_start: 0.8629 (t0) cc_final: 0.8253 (t0) REVERT: F 3 LYS cc_start: 0.6789 (mttt) cc_final: 0.6252 (pptt) REVERT: F 34 ARG cc_start: 0.8976 (ttm-80) cc_final: 0.8575 (mtm110) REVERT: F 191 GLU cc_start: 0.8571 (tt0) cc_final: 0.8244 (tt0) REVERT: G 5 LYS cc_start: 0.4787 (mmmt) cc_final: 0.4003 (pttp) REVERT: G 148 LYS cc_start: 0.7866 (mptt) cc_final: 0.7551 (mttp) REVERT: H 211 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8588 (tt) REVERT: I 438 ASN cc_start: 0.8102 (t0) cc_final: 0.7315 (t0) REVERT: I 477 ILE cc_start: 0.7635 (mm) cc_final: 0.7107 (tp) REVERT: J 155 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7334 (tm-30) REVERT: L 451 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6504 (mtp85) REVERT: L 478 TRP cc_start: 0.8947 (t-100) cc_final: 0.8709 (t-100) REVERT: L 483 ASN cc_start: 0.8766 (m-40) cc_final: 0.8367 (m110) REVERT: L 547 LYS cc_start: 0.8692 (tttt) cc_final: 0.8363 (ttpt) REVERT: L 591 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7263 (mt) REVERT: L 599 TYR cc_start: 0.8442 (t80) cc_final: 0.8133 (t80) REVERT: P 98 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6002 (mtm-85) REVERT: P 112 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: P 131 ASP cc_start: 0.8349 (p0) cc_final: 0.7699 (m-30) REVERT: P 144 PHE cc_start: 0.9327 (m-80) cc_final: 0.8893 (m-10) REVERT: P 191 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7437 (tm-30) outliers start: 90 outliers final: 51 residues processed: 444 average time/residue: 0.1939 time to fit residues: 133.3116 Evaluate side-chains 412 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 B residue 119 HIS 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 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 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 118 LEU Chi-restraints excluded: chain G residue 134 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 337 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 395 LEU 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 J residue 112 GLN 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 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 98 ARG Chi-restraints excluded: chain P residue 112 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 13 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 152 ASN E 32 GLN F 178 ASN H 104 GLN H 335 ASN J 107 ASN J 112 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093066 restraints weight = 38675.918| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.47 r_work: 0.2998 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 26144 Z= 0.335 Angle : 0.737 18.220 35704 Z= 0.358 Chirality : 0.046 0.264 4135 Planarity : 0.005 0.054 4208 Dihedral : 15.426 172.697 4770 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.67 % Allowed : 17.35 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.15), residues: 2964 helix: 0.97 (0.16), residues: 996 sheet: -1.65 (0.20), residues: 550 loop : -1.60 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.019 0.002 TYR K 548 PHE 0.021 0.002 PHE D 103 TRP 0.029 0.002 TRP L 478 HIS 0.005 0.002 HIS P 119 Details of bonding type rmsd covalent geometry : bond 0.00765 (26111) covalent geometry : angle 0.68207 (35662) hydrogen bonds : bond 0.04259 ( 1064) hydrogen bonds : angle 5.06017 ( 3100) metal coordination : bond 0.01508 ( 33) metal coordination : angle 8.13140 ( 42) *********************** 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 482 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 367 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8890 (mp0) cc_final: 0.8665 (mp0) REVERT: B 22 GLU cc_start: 0.8286 (tp30) cc_final: 0.7925 (tp30) REVERT: B 123 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 152 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 25 ARG cc_start: 0.8505 (ttp-170) cc_final: 0.8263 (ttp80) REVERT: C 156 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7724 (ttpp) REVERT: D 72 ASP cc_start: 0.8676 (p0) cc_final: 0.8398 (p0) REVERT: D 152 ASN cc_start: 0.8716 (t0) cc_final: 0.8269 (t0) REVERT: E 3 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8003 (mttt) REVERT: F 34 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8603 (mtm110) REVERT: F 191 GLU cc_start: 0.8612 (tt0) cc_final: 0.8253 (tt0) REVERT: G 5 LYS cc_start: 0.4987 (mmmt) cc_final: 0.4136 (pttp) REVERT: G 108 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7653 (ttmm) REVERT: G 130 GLU cc_start: 0.6037 (tp30) cc_final: 0.5718 (tp30) REVERT: G 134 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (pt) REVERT: G 148 LYS cc_start: 0.7793 (mptt) cc_final: 0.7384 (mttp) REVERT: H 211 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8598 (tt) REVERT: H 310 VAL cc_start: 0.8201 (t) cc_final: 0.7992 (t) REVERT: I 438 ASN cc_start: 0.8162 (t0) cc_final: 0.7341 (t0) REVERT: I 473 TRP cc_start: 0.7960 (t-100) cc_final: 0.7733 (t-100) REVERT: J 72 ASP cc_start: 0.8530 (t70) cc_final: 0.8250 (t70) REVERT: J 140 GLU cc_start: 0.8947 (mp0) cc_final: 0.8648 (mp0) REVERT: L 451 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6678 (mtp85) REVERT: L 483 ASN cc_start: 0.8848 (m-40) cc_final: 0.8448 (m110) REVERT: L 547 LYS cc_start: 0.8739 (tttt) cc_final: 0.8430 (ttpt) REVERT: L 591 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7328 (mt) REVERT: P 112 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: P 123 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7234 (mt-10) REVERT: P 131 ASP cc_start: 0.8364 (p0) cc_final: 0.7627 (m-30) REVERT: P 183 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6499 (mpp-170) outliers start: 115 outliers final: 73 residues processed: 444 average time/residue: 0.1811 time to fit residues: 125.2368 Evaluate side-chains 427 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 345 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 20 THR 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 B residue 152 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 156 LYS 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 108 ASP 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 187 GLU Chi-restraints excluded: chain E residue 188 VAL 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 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 2 ILE 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 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 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 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 421 GLU 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 449 SER Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 588 LEU Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain L residue 591 ILE 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 163 SER 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 162 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 116 optimal weight: 50.0000 chunk 188 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 10 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 32 GLN F 178 ASN H 101 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096356 restraints weight = 38208.321| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.23 r_work: 0.3097 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26144 Z= 0.124 Angle : 0.595 15.370 35704 Z= 0.293 Chirality : 0.041 0.281 4135 Planarity : 0.003 0.041 4208 Dihedral : 15.482 177.558 4770 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.37 % Allowed : 18.65 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 2964 helix: 1.29 (0.16), residues: 1005 sheet: -1.51 (0.20), residues: 552 loop : -1.42 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.015 0.001 TYR J 181 PHE 0.016 0.001 PHE H 137 TRP 0.030 0.001 TRP L 478 HIS 0.004 0.001 HIS K 553 Details of bonding type rmsd covalent geometry : bond 0.00267 (26111) covalent geometry : angle 0.55482 (35662) hydrogen bonds : bond 0.03687 ( 1064) hydrogen bonds : angle 4.69998 ( 3100) metal coordination : bond 0.00677 ( 33) metal coordination : angle 6.31417 ( 42) *********************** 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 473 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 390 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7715 (mtp) REVERT: A 116 GLU cc_start: 0.8903 (mp0) cc_final: 0.8684 (mp0) REVERT: A 144 PHE cc_start: 0.8322 (m-10) cc_final: 0.7913 (m-10) REVERT: A 187 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7427 (mp0) REVERT: B 22 GLU cc_start: 0.8212 (tp30) cc_final: 0.7876 (tp30) REVERT: B 116 GLU cc_start: 0.7664 (tt0) cc_final: 0.7388 (mp0) REVERT: B 123 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 25 ARG cc_start: 0.8512 (ttp-170) cc_final: 0.8241 (ttp80) REVERT: D 72 ASP cc_start: 0.8626 (p0) cc_final: 0.8356 (p0) REVERT: D 111 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: D 152 ASN cc_start: 0.8688 (t0) cc_final: 0.8218 (t0) REVERT: E 150 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8875 (mm) REVERT: F 3 LYS cc_start: 0.6635 (mttt) cc_final: 0.6107 (pptt) REVERT: F 34 ARG cc_start: 0.8947 (ttm-80) cc_final: 0.8618 (mtm110) REVERT: G 5 LYS cc_start: 0.4994 (mmmt) cc_final: 0.4140 (pttp) REVERT: G 83 LEU cc_start: 0.7066 (mp) cc_final: 0.6763 (mm) REVERT: G 108 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7668 (ttmm) REVERT: G 130 GLU cc_start: 0.6179 (tp30) cc_final: 0.5849 (tp30) REVERT: G 134 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (pt) REVERT: G 148 LYS cc_start: 0.7877 (mptt) cc_final: 0.7507 (mttp) REVERT: H 31 ILE cc_start: 0.8767 (pp) cc_final: 0.8525 (pp) REVERT: H 103 ILE cc_start: 0.8611 (mm) cc_final: 0.8409 (mm) REVERT: H 158 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7814 (mt-10) REVERT: H 211 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (tt) REVERT: I 438 ASN cc_start: 0.8166 (t0) cc_final: 0.7373 (t0) REVERT: I 551 GLN cc_start: 0.8573 (tt0) cc_final: 0.8363 (tm-30) REVERT: J 72 ASP cc_start: 0.8393 (t70) cc_final: 0.8098 (t70) REVERT: L 451 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6490 (mtp85) REVERT: L 465 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.5785 (mtp85) REVERT: L 467 GLU cc_start: 0.7363 (pm20) cc_final: 0.7083 (pm20) REVERT: L 483 ASN cc_start: 0.8776 (m-40) cc_final: 0.8393 (m-40) REVERT: L 547 LYS cc_start: 0.8673 (tttt) cc_final: 0.8365 (ttpt) REVERT: P 112 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: P 123 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7172 (mt-10) REVERT: P 131 ASP cc_start: 0.8376 (p0) cc_final: 0.7682 (m-30) REVERT: P 169 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8328 (mm-30) REVERT: P 183 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6414 (mpp-170) REVERT: P 191 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7549 (tm-30) outliers start: 83 outliers final: 52 residues processed: 440 average time/residue: 0.1833 time to fit residues: 123.7567 Evaluate side-chains 418 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 357 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET 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 B residue 119 HIS 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 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 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 68 SER Chi-restraints excluded: chain H residue 130 ASP 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 257 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL 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 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 421 GLU 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 465 ARG Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG 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 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 113 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 32 GLN F 154 GLN F 178 ASN H 62 HIS J 107 ASN J 112 GLN J 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094364 restraints weight = 38454.413| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.23 r_work: 0.3068 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26144 Z= 0.192 Angle : 0.621 15.150 35704 Z= 0.304 Chirality : 0.043 0.424 4135 Planarity : 0.004 0.041 4208 Dihedral : 15.397 176.336 4767 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.74 % Allowed : 18.85 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 2964 helix: 1.37 (0.16), residues: 1007 sheet: -1.46 (0.21), residues: 544 loop : -1.34 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 197 TYR 0.015 0.001 TYR G 161 PHE 0.023 0.002 PHE L 538 TRP 0.027 0.002 TRP L 478 HIS 0.004 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00438 (26111) covalent geometry : angle 0.58077 (35662) hydrogen bonds : bond 0.03667 ( 1064) hydrogen bonds : angle 4.65909 ( 3100) metal coordination : bond 0.00894 ( 33) metal coordination : angle 6.42405 ( 42) *********************** 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 454 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 362 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8027 (ttm) cc_final: 0.7799 (mtp) REVERT: A 68 GLU cc_start: 0.5564 (mp0) cc_final: 0.5353 (mp0) REVERT: A 187 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7274 (mp0) REVERT: B 22 GLU cc_start: 0.8233 (tp30) cc_final: 0.7894 (tp30) REVERT: B 123 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 25 ARG cc_start: 0.8473 (ttp-170) cc_final: 0.8185 (ttp80) REVERT: D 72 ASP cc_start: 0.8634 (p0) cc_final: 0.8371 (p0) REVERT: D 152 ASN cc_start: 0.8700 (t0) cc_final: 0.8193 (t0) REVERT: E 150 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8861 (mm) REVERT: F 3 LYS cc_start: 0.6655 (mttt) cc_final: 0.6105 (pptt) REVERT: G 5 LYS cc_start: 0.4940 (mmmt) cc_final: 0.4113 (pttp) REVERT: G 83 LEU cc_start: 0.7088 (mp) cc_final: 0.6772 (mm) REVERT: G 108 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: G 130 GLU cc_start: 0.6225 (tp30) cc_final: 0.5886 (tp30) REVERT: G 148 LYS cc_start: 0.7809 (mptt) cc_final: 0.7456 (mttp) REVERT: H 62 HIS cc_start: 0.9036 (p-80) cc_final: 0.8284 (p90) REVERT: H 103 ILE cc_start: 0.8604 (mm) cc_final: 0.8374 (mm) REVERT: H 158 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 211 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8639 (tt) REVERT: I 438 ASN cc_start: 0.8248 (t0) cc_final: 0.7559 (t0) REVERT: I 551 GLN cc_start: 0.8659 (tt0) cc_final: 0.8359 (tm-30) REVERT: J 72 ASP cc_start: 0.8413 (t70) cc_final: 0.8114 (t70) REVERT: K 116 ASP cc_start: 0.7315 (m-30) cc_final: 0.6940 (p0) REVERT: L 451 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6541 (mtp85) REVERT: L 465 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.5822 (mtp85) REVERT: L 467 GLU cc_start: 0.7347 (pm20) cc_final: 0.6986 (pm20) REVERT: L 478 TRP cc_start: 0.8761 (t-100) cc_final: 0.8401 (t-100) REVERT: L 483 ASN cc_start: 0.8812 (m-40) cc_final: 0.8406 (m-40) REVERT: L 547 LYS cc_start: 0.8651 (tttt) cc_final: 0.8321 (ttpt) REVERT: P 98 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5943 (mtm-85) REVERT: P 112 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: P 169 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8319 (mm-30) REVERT: P 183 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6458 (mpp-170) outliers start: 92 outliers final: 63 residues processed: 425 average time/residue: 0.1758 time to fit residues: 114.8172 Evaluate side-chains 417 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 119 HIS 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 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 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 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 I residue 441 THR 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 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 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 421 GLU 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 505 LEU 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 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 588 LEU 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 303 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 chunk 160 optimal weight: 0.0470 chunk 2 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 32 GLN F 154 GLN F 178 ASN H 101 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 = 0.3816 r_free = 0.3816 target = 0.140396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097181 restraints weight = 38158.904| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.24 r_work: 0.3112 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26144 Z= 0.123 Angle : 0.579 13.473 35704 Z= 0.286 Chirality : 0.041 0.362 4135 Planarity : 0.003 0.039 4208 Dihedral : 15.445 178.896 4767 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.74 % Allowed : 19.18 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 2964 helix: 1.51 (0.16), residues: 1011 sheet: -1.39 (0.21), residues: 555 loop : -1.20 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 83 TYR 0.015 0.001 TYR P 181 PHE 0.021 0.001 PHE G 14 TRP 0.019 0.001 TRP L 478 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00273 (26111) covalent geometry : angle 0.54658 (35662) hydrogen bonds : bond 0.03483 ( 1064) hydrogen bonds : angle 4.49368 ( 3100) metal coordination : bond 0.00584 ( 33) metal coordination : angle 5.56350 ( 42) *********************** 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 472 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 380 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8014 (ttm) cc_final: 0.7803 (mtp) REVERT: A 68 GLU cc_start: 0.5758 (mp0) cc_final: 0.5544 (mp0) REVERT: A 77 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: A 93 MET cc_start: 0.8495 (tpp) cc_final: 0.8282 (mmm) REVERT: A 187 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7300 (mp0) REVERT: B 9 TYR cc_start: 0.8649 (m-80) cc_final: 0.8445 (m-80) REVERT: B 22 GLU cc_start: 0.8222 (tp30) cc_final: 0.7902 (tp30) REVERT: B 116 GLU cc_start: 0.7610 (tt0) cc_final: 0.7370 (mp0) REVERT: B 123 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 25 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.8204 (ttp80) REVERT: D 72 ASP cc_start: 0.8642 (p0) cc_final: 0.8398 (p0) REVERT: D 111 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: D 152 ASN cc_start: 0.8732 (t0) cc_final: 0.8212 (t0) REVERT: E 3 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8001 (mttt) REVERT: E 150 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8812 (mm) REVERT: F 3 LYS cc_start: 0.6612 (mttt) cc_final: 0.6059 (pptt) REVERT: G 5 LYS cc_start: 0.4962 (mmmt) cc_final: 0.4145 (pttp) REVERT: G 83 LEU cc_start: 0.7156 (mp) cc_final: 0.6861 (mm) REVERT: G 96 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7534 (p) REVERT: G 108 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7688 (ttmm) REVERT: G 148 LYS cc_start: 0.7878 (mptt) cc_final: 0.7526 (mttp) REVERT: H 31 ILE cc_start: 0.8769 (pp) cc_final: 0.8495 (pp) REVERT: H 103 ILE cc_start: 0.8605 (mm) cc_final: 0.8231 (mm) REVERT: H 158 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7825 (mt-10) REVERT: H 211 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8743 (tt) REVERT: H 234 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8268 (ttm-80) REVERT: H 594 ASP cc_start: 0.7882 (m-30) cc_final: 0.7452 (p0) REVERT: I 453 MET cc_start: 0.8276 (ttt) cc_final: 0.8051 (ttt) REVERT: I 485 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6542 (mmp) REVERT: I 551 GLN cc_start: 0.8645 (tt0) cc_final: 0.8374 (tm-30) REVERT: J 72 ASP cc_start: 0.8306 (t70) cc_final: 0.8028 (t70) REVERT: K 116 ASP cc_start: 0.7247 (m-30) cc_final: 0.6869 (p0) REVERT: L 451 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6564 (mtp85) REVERT: L 465 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.5996 (mtp85) REVERT: L 467 GLU cc_start: 0.7393 (pm20) cc_final: 0.7000 (pm20) REVERT: L 483 ASN cc_start: 0.8748 (m-40) cc_final: 0.8292 (m-40) REVERT: L 486 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7567 (mtp85) REVERT: L 547 LYS cc_start: 0.8608 (tttt) cc_final: 0.8284 (ttpt) REVERT: P 98 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6186 (mtm-85) REVERT: P 112 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: P 131 ASP cc_start: 0.8083 (p0) cc_final: 0.7275 (m-30) REVERT: P 169 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8358 (mm-30) REVERT: P 183 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6491 (mpp-170) outliers start: 92 outliers final: 54 residues processed: 437 average time/residue: 0.1788 time to fit residues: 120.9455 Evaluate side-chains 423 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 119 HIS 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 84 CYS 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 108 LYS 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 234 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 450 TYR 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 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 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 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 98 ARG Chi-restraints excluded: chain P residue 106 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 16 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 272 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 overall best weight: 2.9524 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092955 restraints weight = 38155.503| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.21 r_work: 0.3047 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 26144 Z= 0.244 Angle : 0.660 15.199 35704 Z= 0.323 Chirality : 0.044 0.327 4135 Planarity : 0.004 0.047 4208 Dihedral : 15.331 174.990 4767 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.70 % Allowed : 20.03 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 2964 helix: 1.47 (0.16), residues: 1006 sheet: -1.31 (0.21), residues: 559 loop : -1.23 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 197 TYR 0.013 0.001 TYR K 548 PHE 0.023 0.002 PHE D 103 TRP 0.033 0.002 TRP L 478 HIS 0.005 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00557 (26111) covalent geometry : angle 0.62024 (35662) hydrogen bonds : bond 0.03782 ( 1064) hydrogen bonds : angle 4.61050 ( 3100) metal coordination : bond 0.01098 ( 33) metal coordination : angle 6.58769 ( 42) *********************** 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 458 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 367 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7975 (ttm) cc_final: 0.7737 (mtp) REVERT: A 68 GLU cc_start: 0.5816 (mp0) cc_final: 0.5577 (mp0) REVERT: A 77 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8212 (mtt90) REVERT: A 187 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7197 (mp0) REVERT: B 9 TYR cc_start: 0.8655 (m-80) cc_final: 0.8421 (m-80) REVERT: B 22 GLU cc_start: 0.8242 (tp30) cc_final: 0.7895 (tp30) REVERT: B 123 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7058 (tm-30) REVERT: C 25 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.8267 (ttp80) REVERT: D 72 ASP cc_start: 0.8656 (p0) cc_final: 0.8397 (p0) REVERT: D 152 ASN cc_start: 0.8706 (t0) cc_final: 0.8170 (t0) REVERT: E 3 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: E 150 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8889 (mm) REVERT: F 3 LYS cc_start: 0.6695 (mttt) cc_final: 0.6157 (pptt) REVERT: G 5 LYS cc_start: 0.5016 (mmmt) cc_final: 0.4183 (pttp) REVERT: G 83 LEU cc_start: 0.7227 (mp) cc_final: 0.6941 (mm) REVERT: G 96 VAL cc_start: 0.7969 (m) cc_final: 0.7467 (p) REVERT: G 108 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7592 (ttmm) REVERT: G 148 LYS cc_start: 0.7807 (mptt) cc_final: 0.7516 (mttp) REVERT: H 1 MET cc_start: 0.7885 (mpp) cc_final: 0.7572 (pmm) REVERT: H 103 ILE cc_start: 0.8519 (mm) cc_final: 0.8215 (mm) REVERT: H 234 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8270 (ttm-80) REVERT: H 594 ASP cc_start: 0.7915 (m-30) cc_final: 0.7423 (p0) REVERT: I 438 ASN cc_start: 0.8227 (t0) cc_final: 0.7613 (t0) REVERT: I 551 GLN cc_start: 0.8644 (tt0) cc_final: 0.8376 (tm-30) REVERT: J 72 ASP cc_start: 0.8496 (t70) cc_final: 0.8256 (t70) REVERT: K 116 ASP cc_start: 0.7215 (m-30) cc_final: 0.6851 (p0) REVERT: K 145 ASN cc_start: 0.8072 (p0) cc_final: 0.7826 (p0) REVERT: L 451 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6789 (mtp85) REVERT: L 465 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7462 (mpp80) REVERT: L 467 GLU cc_start: 0.7434 (pm20) cc_final: 0.7095 (pm20) REVERT: L 479 ASN cc_start: 0.8108 (m-40) cc_final: 0.7874 (m-40) REVERT: L 483 ASN cc_start: 0.8812 (m-40) cc_final: 0.8372 (m-40) REVERT: L 547 LYS cc_start: 0.8608 (tttt) cc_final: 0.8278 (ttpt) REVERT: P 98 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6362 (mtm-85) REVERT: P 112 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: P 131 ASP cc_start: 0.8098 (p0) cc_final: 0.7295 (m-30) REVERT: P 183 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.6527 (mpp-170) outliers start: 91 outliers final: 66 residues processed: 426 average time/residue: 0.1834 time to fit residues: 121.1724 Evaluate side-chains 431 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG 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 62 MET 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 C residue 118 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 3 LYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 84 CYS 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 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 130 ASP 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 219 CYS Chi-restraints excluded: chain H residue 234 ARG 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 464 ASP 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 I residue 604 ASN 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 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 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 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 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 59 optimal weight: 0.7980 chunk 119 optimal weight: 0.0970 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN H 101 GLN I 443 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 = 0.3822 r_free = 0.3822 target = 0.140997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098091 restraints weight = 38229.297| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.22 r_work: 0.3117 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26144 Z= 0.119 Angle : 0.587 12.862 35704 Z= 0.290 Chirality : 0.041 0.286 4135 Planarity : 0.003 0.039 4208 Dihedral : 15.368 179.256 4765 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.89 % Allowed : 20.72 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.15), residues: 2964 helix: 1.59 (0.16), residues: 1011 sheet: -1.27 (0.21), residues: 560 loop : -1.15 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 451 TYR 0.017 0.001 TYR H 245 PHE 0.031 0.001 PHE L 538 TRP 0.024 0.001 TRP L 478 HIS 0.005 0.001 HIS K 553 Details of bonding type rmsd covalent geometry : bond 0.00261 (26111) covalent geometry : angle 0.55811 (35662) hydrogen bonds : bond 0.03489 ( 1064) hydrogen bonds : angle 4.41868 ( 3100) metal coordination : bond 0.00518 ( 33) metal coordination : angle 5.34316 ( 42) *********************** 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 444 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 373 time to evaluate : 1.074 Fit side-chains REVERT: A 62 MET cc_start: 0.7965 (ttm) cc_final: 0.7742 (mtp) REVERT: A 68 GLU cc_start: 0.5849 (mp0) cc_final: 0.5608 (mp0) REVERT: A 77 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8212 (mtt90) REVERT: A 187 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7280 (mp0) REVERT: B 9 TYR cc_start: 0.8614 (m-80) cc_final: 0.8408 (m-80) REVERT: B 22 GLU cc_start: 0.8212 (tp30) cc_final: 0.7881 (tp30) REVERT: B 123 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6998 (tp30) REVERT: C 25 ARG cc_start: 0.8517 (ttp-170) cc_final: 0.8209 (ttp80) REVERT: D 72 ASP cc_start: 0.8625 (p0) cc_final: 0.8389 (p0) REVERT: D 111 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: D 152 ASN cc_start: 0.8714 (t0) cc_final: 0.8175 (t0) REVERT: E 150 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8818 (mm) REVERT: F 3 LYS cc_start: 0.6564 (mttt) cc_final: 0.6055 (pptt) REVERT: G 5 LYS cc_start: 0.5027 (mmmt) cc_final: 0.4259 (pttp) REVERT: G 75 TYR cc_start: 0.7894 (m-10) cc_final: 0.7540 (m-80) REVERT: G 83 LEU cc_start: 0.7161 (mp) cc_final: 0.6875 (mm) REVERT: G 108 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7611 (ttmm) REVERT: G 134 ILE cc_start: 0.8727 (mm) cc_final: 0.8343 (pt) REVERT: G 148 LYS cc_start: 0.7843 (mptt) cc_final: 0.7541 (mttp) REVERT: H 1 MET cc_start: 0.7730 (mpp) cc_final: 0.7347 (pmm) REVERT: H 103 ILE cc_start: 0.8564 (mm) cc_final: 0.8226 (mm) REVERT: H 158 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7795 (mt-10) REVERT: H 234 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8195 (ttm-80) REVERT: H 594 ASP cc_start: 0.7829 (m-30) cc_final: 0.7399 (p0) REVERT: I 438 ASN cc_start: 0.8123 (t0) cc_final: 0.7590 (t0) REVERT: I 485 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6547 (mmp) REVERT: I 551 GLN cc_start: 0.8708 (tt0) cc_final: 0.8391 (tm-30) REVERT: J 72 ASP cc_start: 0.8344 (t70) cc_final: 0.8082 (t70) REVERT: J 196 ASP cc_start: 0.8582 (p0) cc_final: 0.8327 (p0) REVERT: K 116 ASP cc_start: 0.7261 (m-30) cc_final: 0.6900 (p0) REVERT: L 451 ARG cc_start: 0.7289 (mtp180) cc_final: 0.6645 (mtp85) REVERT: L 465 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7562 (mpp80) REVERT: L 467 GLU cc_start: 0.7435 (pm20) cc_final: 0.7103 (pm20) REVERT: L 483 ASN cc_start: 0.8742 (m-40) cc_final: 0.8285 (m-40) REVERT: L 486 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7558 (mtp85) REVERT: L 547 LYS cc_start: 0.8608 (tttt) cc_final: 0.8276 (ttpt) REVERT: L 577 GLU cc_start: 0.8825 (tp30) cc_final: 0.8622 (mm-30) REVERT: P 98 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.5648 (ptp90) REVERT: P 112 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: P 131 ASP cc_start: 0.8045 (p0) cc_final: 0.7563 (p0) REVERT: P 169 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8362 (mm-30) REVERT: P 183 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6453 (mpp-170) outliers start: 71 outliers final: 52 residues processed: 416 average time/residue: 0.1984 time to fit residues: 127.4118 Evaluate side-chains 415 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 157 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 118 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 84 CYS 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 13 LYS Chi-restraints excluded: chain F residue 89 LEU 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 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 130 ASP 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 234 ARG Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 452 LEU 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 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 450 TYR 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 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 112 GLN Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 165 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN F 45 ASN K 145 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 = 0.3812 r_free = 0.3812 target = 0.140167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097013 restraints weight = 38245.443| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.22 r_work: 0.3099 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26144 Z= 0.146 Angle : 0.605 12.943 35704 Z= 0.299 Chirality : 0.042 0.339 4135 Planarity : 0.003 0.040 4208 Dihedral : 15.280 178.222 4765 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 21.13 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 2964 helix: 1.63 (0.16), residues: 1011 sheet: -1.18 (0.21), residues: 549 loop : -1.15 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 361 TYR 0.016 0.001 TYR H 245 PHE 0.030 0.001 PHE K 166 TRP 0.023 0.001 TRP L 478 HIS 0.005 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00330 (26111) covalent geometry : angle 0.57566 (35662) hydrogen bonds : bond 0.03468 ( 1064) hydrogen bonds : angle 4.39397 ( 3100) metal coordination : bond 0.00634 ( 33) metal coordination : angle 5.46508 ( 42) ********************** 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 438 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 370 time to evaluate : 1.033 Fit side-chains REVERT: A 62 MET cc_start: 0.7966 (ttm) cc_final: 0.7740 (mtp) REVERT: A 68 GLU cc_start: 0.5822 (mp0) cc_final: 0.5560 (mp0) REVERT: A 77 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8251 (mtt90) REVERT: A 144 PHE cc_start: 0.8309 (m-10) cc_final: 0.7963 (m-10) REVERT: A 187 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7201 (mp0) REVERT: B 22 GLU cc_start: 0.8223 (tp30) cc_final: 0.7891 (tp30) REVERT: B 25 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7348 (tmm-80) REVERT: B 123 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 25 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.8121 (ttp80) REVERT: D 72 ASP cc_start: 0.8632 (p0) cc_final: 0.8408 (p0) REVERT: D 111 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: D 152 ASN cc_start: 0.8769 (t0) cc_final: 0.8236 (t0) REVERT: E 150 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8818 (mm) REVERT: F 3 LYS cc_start: 0.6614 (mttt) cc_final: 0.6168 (pptt) REVERT: G 5 LYS cc_start: 0.5035 (mmmt) cc_final: 0.4268 (pttp) REVERT: G 75 TYR cc_start: 0.7922 (m-10) cc_final: 0.7584 (m-80) REVERT: G 83 LEU cc_start: 0.7167 (mp) cc_final: 0.6886 (mm) REVERT: G 108 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7672 (ttmm) REVERT: G 148 LYS cc_start: 0.7800 (mptt) cc_final: 0.7489 (mttp) REVERT: H 1 MET cc_start: 0.7849 (mpp) cc_final: 0.7347 (pmm) REVERT: H 103 ILE cc_start: 0.8573 (mm) cc_final: 0.8235 (mm) REVERT: H 158 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 234 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: H 594 ASP cc_start: 0.7844 (m-30) cc_final: 0.7419 (p0) REVERT: I 438 ASN cc_start: 0.8058 (t0) cc_final: 0.7550 (t0) REVERT: I 485 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6493 (mmp) REVERT: I 551 GLN cc_start: 0.8706 (tt0) cc_final: 0.8411 (tm-30) REVERT: J 72 ASP cc_start: 0.8356 (t70) cc_final: 0.8114 (t70) REVERT: J 196 ASP cc_start: 0.8587 (p0) cc_final: 0.8336 (p0) REVERT: L 438 ASN cc_start: 0.7847 (t0) cc_final: 0.7616 (t0) REVERT: L 451 ARG cc_start: 0.7401 (mtp180) cc_final: 0.6758 (mtp85) REVERT: L 465 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7560 (mpp80) REVERT: L 467 GLU cc_start: 0.7425 (pm20) cc_final: 0.7098 (pm20) REVERT: L 483 ASN cc_start: 0.8741 (m-40) cc_final: 0.8284 (m-40) REVERT: L 486 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7618 (mtp85) REVERT: L 547 LYS cc_start: 0.8628 (tttt) cc_final: 0.8295 (ttpt) REVERT: L 577 GLU cc_start: 0.8833 (tp30) cc_final: 0.8623 (mm-30) REVERT: P 98 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6351 (mtm-85) REVERT: P 112 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: P 131 ASP cc_start: 0.8033 (p0) cc_final: 0.7554 (p0) REVERT: P 169 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8313 (mm-30) REVERT: P 181 TYR cc_start: 0.9109 (m-80) cc_final: 0.8850 (m-80) REVERT: P 183 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6498 (mpp-170) outliers start: 68 outliers final: 54 residues processed: 412 average time/residue: 0.2015 time to fit residues: 128.6861 Evaluate side-chains 424 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 360 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 MET Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 118 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 84 CYS 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 13 LYS Chi-restraints excluded: chain F residue 89 LEU 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 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 130 ASP 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 234 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 476 MET Chi-restraints excluded: chain I residue 452 LEU 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 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 145 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 450 TYR 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 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 112 GLN Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 183 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 223 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 0.0770 chunk 270 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN F 45 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 = 0.3821 r_free = 0.3821 target = 0.140953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097766 restraints weight = 38193.749| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26144 Z= 0.126 Angle : 0.594 12.633 35704 Z= 0.294 Chirality : 0.041 0.319 4135 Planarity : 0.003 0.038 4208 Dihedral : 15.280 178.846 4765 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.72 % Allowed : 21.17 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 2964 helix: 1.67 (0.16), residues: 1012 sheet: -1.19 (0.21), residues: 563 loop : -1.15 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 361 TYR 0.017 0.001 TYR J 181 PHE 0.033 0.001 PHE K 166 TRP 0.019 0.001 TRP L 535 HIS 0.005 0.001 HIS K 553 Details of bonding type rmsd covalent geometry : bond 0.00280 (26111) covalent geometry : angle 0.56653 (35662) hydrogen bonds : bond 0.03415 ( 1064) hydrogen bonds : angle 4.33789 ( 3100) metal coordination : bond 0.00542 ( 33) metal coordination : angle 5.21643 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.37 seconds wall clock time: 124 minutes 36.00 seconds (7476.00 seconds total)