Starting phenix.real_space_refine on Sun Jul 5 03:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857.map" model { file = "/net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z99_39857/07_2026/8z99_39857_neut.cif" } 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-dev-6108/lib/python3.11/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: 5.88, per 1000 atoms: 0.23 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 87 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 71 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 84 " Number of angles added : 42 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5692 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 39 sheets defined 36.2% alpha, 18.7% beta 26 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.03 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: 5.22 Time building geometry restraints manager: 2.83 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.120 Find NCS groups from input model: 0.470 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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= 0.548 Angle : 1.338 28.858 35704 Z= 0.797 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 are 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/Z covalent geometry : bond 0.00904 / 0.54 (26111) covalent geometry : angle 1.26815 / 0.79 (35662) hydrogen bonds : bond 0.15920 / 10.74 ( 1064) hydrogen bonds : angle 7.67319 / 5.34 ( 3100) metal coordination : bond 0.06471 / 5.22 ( 33) metal coordination : angle 12.47344 / 8.06 ( 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 : 1.004 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: 0.1938 time to fit residues: 153.8672 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 : 0.642 ------------------------------------------------------------------------------- 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... A 45 ASN B 112 GLN E 107 ASN F 154 GLN F 178 ASN H 236 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 ASN ** 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 = 0.3838 r_free = 0.3838 target = 0.142596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099901 restraints weight = 38471.988| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.22 r_work: 0.3146 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26144 Z= 0.160 Angle : 0.676 23.704 35704 Z= 0.341 Chirality : 0.043 0.291 4135 Planarity : 0.005 0.060 4208 Dihedral : 15.891 176.314 4799 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.93 % Allowed : 16.98 % Favored : 80.09 % 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 are not related in a simple way. whole: -1.59 (0.14), residues: 2964 helix: 0.50 (0.16), residues: 989 sheet: -1.89 (0.20), residues: 533 loop : -1.84 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.016 0.001 TYR K 548 PHE 0.021 0.002 PHE E 167 TRP 0.035 0.002 TRP L 478 HIS 0.009 0.001 HIS L 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (26111) covalent geometry : angle 0.61404 / 0.34 (35662) hydrogen bonds : bond 0.04898 / 3.32 ( 1064) hydrogen bonds : angle 5.58033 / 3.92 ( 3100) metal coordination : bond 0.01169 / 0.80 ( 33) metal coordination : angle 8.24921 / 5.29 ( 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 475 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 403 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 144 PHE cc_start: 0.8230 (m-10) cc_final: 0.7813 (m-10) REVERT: B 112 GLN cc_start: 0.8284 (mt0) cc_final: 0.8064 (mt0) REVERT: B 152 ASN cc_start: 0.8524 (p0) cc_final: 0.7880 (p0) REVERT: B 196 ASP cc_start: 0.8851 (p0) cc_final: 0.8633 (p0) REVERT: D 72 ASP cc_start: 0.8509 (p0) cc_final: 0.8154 (p0) REVERT: D 111 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: D 116 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 3 LYS cc_start: 0.6764 (mttt) cc_final: 0.6228 (pptt) REVERT: F 34 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8547 (mtm110) REVERT: F 191 GLU cc_start: 0.8487 (tt0) cc_final: 0.8073 (tt0) REVERT: G 5 LYS cc_start: 0.4849 (OUTLIER) cc_final: 0.4223 (pttp) REVERT: G 148 LYS cc_start: 0.7886 (mptt) cc_final: 0.7685 (mmtp) REVERT: H 62 HIS cc_start: 0.8560 (p-80) cc_final: 0.8210 (p90) REVERT: H 65 LEU cc_start: 0.8470 (mt) cc_final: 0.8231 (mp) REVERT: H 211 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8560 (tt) REVERT: I 438 ASN cc_start: 0.8009 (t0) cc_final: 0.7236 (t0) REVERT: I 453 MET cc_start: 0.8324 (ttt) cc_final: 0.8121 (ttt) REVERT: I 568 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8331 (tt0) REVERT: K 468 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7219 (mm) REVERT: K 485 MET cc_start: 0.9134 (mmm) cc_final: 0.8587 (mmt) REVERT: K 584 TYR cc_start: 0.8546 (t80) cc_final: 0.8220 (t80) REVERT: L 451 ARG cc_start: 0.6752 (mtp180) cc_final: 0.6272 (mtp85) REVERT: L 483 ASN cc_start: 0.8678 (m-40) cc_final: 0.8310 (m-40) REVERT: L 547 LYS cc_start: 0.8689 (tttt) cc_final: 0.8429 (ttpt) REVERT: L 587 LEU cc_start: 0.8378 (mm) cc_final: 0.7908 (mm) REVERT: L 599 TYR cc_start: 0.8344 (t80) cc_final: 0.7962 (t80) REVERT: P 112 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: P 131 ASP cc_start: 0.8302 (p0) cc_final: 0.7687 (m-30) REVERT: P 144 PHE cc_start: 0.9225 (m-80) cc_final: 0.8777 (m-10) outliers start: 72 outliers final: 37 residues processed: 446 average time/residue: 0.1767 time to fit residues: 123.2043 Evaluate side-chains 408 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 365 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 E residue 199 LEU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU 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 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 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: 0.5980 chunk 86 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 269 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN E 32 GLN E 171 ASN F 178 ASN H 269 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** P 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099266 restraints weight = 38612.827| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.23 r_work: 0.3135 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 26144 Z= 0.149 Angle : 0.610 17.185 35704 Z= 0.307 Chirality : 0.042 0.312 4135 Planarity : 0.004 0.049 4208 Dihedral : 15.644 176.606 4777 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.25 % Allowed : 17.23 % Favored : 79.52 % 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 are not related in a simple way. whole: -1.11 (0.15), residues: 2964 helix: 1.00 (0.16), residues: 998 sheet: -1.67 (0.20), residues: 540 loop : -1.61 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 561 TYR 0.014 0.001 TYR F 19 PHE 0.021 0.002 PHE K 166 TRP 0.034 0.002 TRP L 478 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (26111) covalent geometry : angle 0.55794 / 0.30 (35662) hydrogen bonds : bond 0.04381 / 2.94 ( 1064) hydrogen bonds : angle 5.09303 / 3.56 ( 3100) metal coordination : bond 0.01004 / 0.60 ( 33) metal coordination : angle 7.18703 / 4.61 ( 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 467 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 387 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7972 (ttm) cc_final: 0.7769 (mtp) REVERT: A 105 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 144 PHE cc_start: 0.8205 (m-10) cc_final: 0.7835 (m-10) REVERT: B 22 GLU cc_start: 0.8160 (tp30) cc_final: 0.7928 (tp30) REVERT: B 152 ASN cc_start: 0.8606 (p0) cc_final: 0.8165 (p0) REVERT: D 72 ASP cc_start: 0.8536 (p0) cc_final: 0.8246 (p0) REVERT: F 3 LYS cc_start: 0.6760 (mttt) cc_final: 0.6231 (pptt) REVERT: F 34 ARG cc_start: 0.8958 (ttm-80) cc_final: 0.8605 (mtm110) REVERT: F 191 GLU cc_start: 0.8532 (tt0) cc_final: 0.8236 (tt0) REVERT: G 5 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.4130 (pttp) REVERT: G 148 LYS cc_start: 0.7849 (mptt) cc_final: 0.7402 (mttp) REVERT: H 160 HIS cc_start: 0.8963 (t70) cc_final: 0.8747 (t70) REVERT: H 211 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8566 (tt) REVERT: I 438 ASN cc_start: 0.8083 (t0) cc_final: 0.7281 (t0) REVERT: K 468 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7130 (mm) REVERT: L 451 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6379 (mtp85) REVERT: L 453 MET cc_start: 0.7939 (ttt) cc_final: 0.7733 (ttt) REVERT: L 483 ASN cc_start: 0.8699 (m-40) cc_final: 0.8286 (m-40) REVERT: L 547 LYS cc_start: 0.8680 (tttt) cc_final: 0.8365 (ttpt) REVERT: L 577 GLU cc_start: 0.8774 (tp30) cc_final: 0.8446 (mm-30) REVERT: P 112 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8635 (mt0) REVERT: P 131 ASP cc_start: 0.8306 (p0) cc_final: 0.7639 (m-30) REVERT: P 144 PHE cc_start: 0.9284 (m-80) cc_final: 0.8863 (m-10) outliers start: 80 outliers final: 44 residues processed: 437 average time/residue: 0.1879 time to fit residues: 127.8844 Evaluate side-chains 404 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 355 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 C residue 51 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 2 LYS 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 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 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 I residue 444 MET Chi-restraints excluded: chain I residue 452 LEU 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 441 THR Chi-restraints excluded: chain K residue 468 ILE 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 554 ARG Chi-restraints excluded: chain P residue 109 THR 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: 20.0000 chunk 177 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 303 optimal weight: 0.0970 chunk 171 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095921 restraints weight = 38592.781| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.21 r_work: 0.3084 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26144 Z= 0.214 Angle : 0.631 16.710 35704 Z= 0.316 Chirality : 0.043 0.285 4135 Planarity : 0.004 0.044 4208 Dihedral : 15.523 175.886 4777 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.78 % Allowed : 17.59 % Favored : 78.63 % 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 are not related in a simple way. whole: -0.91 (0.15), residues: 2964 helix: 1.18 (0.16), residues: 994 sheet: -1.59 (0.20), residues: 551 loop : -1.49 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 361 TYR 0.017 0.001 TYR J 181 PHE 0.025 0.002 PHE K 494 TRP 0.051 0.002 TRP L 478 HIS 0.004 0.001 HIS P 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (26111) covalent geometry : angle 0.58200 / 0.31 (35662) hydrogen bonds : bond 0.04248 / 2.84 ( 1064) hydrogen bonds : angle 4.92686 / 3.42 ( 3100) metal coordination : bond 0.01112 / 0.72 ( 33) metal coordination : angle 7.11935 / 4.62 ( 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 466 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 373 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8084 (mt) REVERT: A 144 PHE cc_start: 0.8287 (m-10) cc_final: 0.7858 (m-10) REVERT: B 22 GLU cc_start: 0.8178 (tp30) cc_final: 0.7915 (tp30) REVERT: B 123 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 72 ASP cc_start: 0.8570 (p0) cc_final: 0.8295 (p0) REVERT: D 152 ASN cc_start: 0.8650 (t0) cc_final: 0.8259 (t0) REVERT: F 3 LYS cc_start: 0.6744 (mttt) cc_final: 0.6201 (pptt) REVERT: F 34 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8551 (mtm110) REVERT: F 191 GLU cc_start: 0.8579 (tt0) cc_final: 0.8228 (tt0) REVERT: G 5 LYS cc_start: 0.4762 (mmmt) cc_final: 0.3957 (pttp) REVERT: G 148 LYS cc_start: 0.7794 (mptt) cc_final: 0.7440 (mttp) REVERT: H 135 GLU cc_start: 0.8357 (tp30) cc_final: 0.8142 (tp30) REVERT: H 211 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (tt) REVERT: H 234 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (ttm-80) REVERT: I 438 ASN cc_start: 0.8129 (t0) cc_final: 0.7388 (t0) REVERT: L 451 ARG cc_start: 0.7030 (mtp180) cc_final: 0.6467 (mtp85) REVERT: L 483 ASN cc_start: 0.8781 (m-40) cc_final: 0.8415 (m-40) REVERT: L 547 LYS cc_start: 0.8705 (tttt) cc_final: 0.8376 (ttpt) REVERT: L 599 TYR cc_start: 0.8435 (t80) cc_final: 0.8117 (t80) REVERT: P 112 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: P 131 ASP cc_start: 0.8353 (p0) cc_final: 0.7696 (m-30) REVERT: P 144 PHE cc_start: 0.9317 (m-80) cc_final: 0.8956 (m-10) REVERT: P 191 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 93 outliers final: 56 residues processed: 430 average time/residue: 0.1658 time to fit residues: 111.9007 Evaluate side-chains 410 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 350 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 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 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 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 234 ARG 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 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 116 ASP 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 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 589 SER Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 162 optimal weight: 4.9990 chunk 238 optimal weight: 0.0470 chunk 237 optimal weight: 10.0000 chunk 116 optimal weight: 50.0000 chunk 188 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 304 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 257 optimal weight: 0.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 112 GLN E 32 GLN F 178 ASN I 443 ASN J 107 ASN J 112 GLN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098134 restraints weight = 38174.387| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.23 r_work: 0.3126 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26144 Z= 0.122 Angle : 0.565 15.137 35704 Z= 0.287 Chirality : 0.042 0.312 4135 Planarity : 0.004 0.044 4208 Dihedral : 15.564 178.362 4768 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.13 % Allowed : 18.53 % Favored : 78.34 % 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 are not related in a simple way. whole: -0.72 (0.15), residues: 2964 helix: 1.32 (0.16), residues: 1005 sheet: -1.49 (0.21), residues: 541 loop : -1.39 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 361 TYR 0.016 0.001 TYR G 161 PHE 0.016 0.001 PHE E 167 TRP 0.021 0.001 TRP L 478 HIS 0.003 0.001 HIS K 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26111) covalent geometry : angle 0.52496 / 0.28 (35662) hydrogen bonds : bond 0.03996 / 2.66 ( 1064) hydrogen bonds : angle 4.70671 / 3.27 ( 3100) metal coordination : bond 0.00689 / 0.45 ( 33) metal coordination : angle 6.12739 / 3.93 ( 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 468 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 391 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7977 (ttm) cc_final: 0.7761 (mtp) REVERT: A 105 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 116 GLU cc_start: 0.8952 (mp0) cc_final: 0.8702 (mp0) REVERT: A 144 PHE cc_start: 0.8276 (m-10) cc_final: 0.7880 (m-10) REVERT: B 22 GLU cc_start: 0.8205 (tp30) cc_final: 0.7929 (tp30) REVERT: B 116 GLU cc_start: 0.7544 (tt0) cc_final: 0.7256 (mp0) REVERT: B 123 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 25 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8253 (ttp-170) REVERT: D 72 ASP cc_start: 0.8563 (p0) cc_final: 0.8292 (p0) REVERT: D 111 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: D 152 ASN cc_start: 0.8682 (t0) cc_final: 0.8248 (t0) REVERT: F 3 LYS cc_start: 0.6658 (mttt) cc_final: 0.6174 (pptt) REVERT: F 19 TYR cc_start: 0.9259 (t80) cc_final: 0.8956 (t80) REVERT: F 34 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8582 (mtm110) REVERT: G 5 LYS cc_start: 0.4791 (mmmt) cc_final: 0.3969 (pttp) REVERT: G 130 GLU cc_start: 0.5784 (tp30) cc_final: 0.5476 (tp30) REVERT: G 134 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7725 (pt) REVERT: G 148 LYS cc_start: 0.7857 (mptt) cc_final: 0.7632 (mmtp) REVERT: H 10 LYS cc_start: 0.8326 (ttpp) cc_final: 0.8107 (ttmt) REVERT: H 78 ARG cc_start: 0.8644 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: H 211 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8617 (tt) REVERT: H 234 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8252 (ttm-80) REVERT: I 438 ASN cc_start: 0.8144 (t0) cc_final: 0.7428 (t0) REVERT: L 451 ARG cc_start: 0.6964 (mtp180) cc_final: 0.6400 (mtp85) REVERT: L 483 ASN cc_start: 0.8724 (m-40) cc_final: 0.8314 (m-40) REVERT: L 533 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7904 (mt-10) REVERT: L 536 GLU cc_start: 0.8246 (tp30) cc_final: 0.8027 (tp30) REVERT: L 547 LYS cc_start: 0.8723 (tttt) cc_final: 0.8429 (ttpt) REVERT: L 577 GLU cc_start: 0.8779 (tp30) cc_final: 0.8502 (mm-30) REVERT: L 599 TYR cc_start: 0.8434 (t80) cc_final: 0.8118 (t80) REVERT: P 45 ASN cc_start: 0.7908 (m-40) cc_final: 0.7693 (m-40) REVERT: P 112 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8656 (mt0) REVERT: P 123 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7197 (mt-10) REVERT: P 131 ASP cc_start: 0.8391 (p0) cc_final: 0.7618 (m-30) REVERT: P 144 PHE cc_start: 0.9348 (m-80) cc_final: 0.8989 (m-10) REVERT: P 169 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8295 (mm-30) REVERT: P 191 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7402 (tm-30) outliers start: 77 outliers final: 51 residues processed: 438 average time/residue: 0.1748 time to fit residues: 119.1606 Evaluate side-chains 414 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 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 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 1 MET 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 234 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 460 VAL 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 P residue 109 THR Chi-restraints excluded: chain P residue 112 GLN 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: 0.6980 chunk 292 optimal weight: 9.9990 chunk 119 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 256 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN E 32 GLN F 178 ASN ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 551 GLN I 600 ASN J 107 ASN J 112 GLN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097120 restraints weight = 38334.324| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.23 r_work: 0.3112 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26144 Z= 0.148 Angle : 0.573 14.383 35704 Z= 0.289 Chirality : 0.042 0.294 4135 Planarity : 0.003 0.044 4208 Dihedral : 15.494 177.860 4767 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.29 % Allowed : 18.65 % Favored : 78.06 % 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 are not related in a simple way. whole: -0.66 (0.15), residues: 2964 helix: 1.34 (0.16), residues: 1010 sheet: -1.46 (0.20), residues: 550 loop : -1.32 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 361 TYR 0.016 0.001 TYR G 38 PHE 0.019 0.001 PHE K 122 TRP 0.026 0.001 TRP L 478 HIS 0.004 0.001 HIS F 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (26111) covalent geometry : angle 0.53445 / 0.29 (35662) hydrogen bonds : bond 0.03880 / 2.59 ( 1064) hydrogen bonds : angle 4.62055 / 3.21 ( 3100) metal coordination : bond 0.00758 / 0.49 ( 33) metal coordination : angle 6.04402 / 3.88 ( 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 453 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7988 (ttm) cc_final: 0.7738 (mtp) REVERT: A 87 CYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7054 (m) REVERT: A 105 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 116 GLU cc_start: 0.8864 (mp0) cc_final: 0.8638 (mp0) REVERT: A 144 PHE cc_start: 0.8282 (m-10) cc_final: 0.7865 (m-10) REVERT: B 22 GLU cc_start: 0.8212 (tp30) cc_final: 0.7950 (tp30) REVERT: B 116 GLU cc_start: 0.7620 (tt0) cc_final: 0.7296 (mp0) REVERT: B 123 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7142 (tm-30) REVERT: D 72 ASP cc_start: 0.8611 (p0) cc_final: 0.8341 (p0) REVERT: D 152 ASN cc_start: 0.8719 (t0) cc_final: 0.8266 (t0) REVERT: E 3 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8089 (mttt) REVERT: F 3 LYS cc_start: 0.6625 (mttt) cc_final: 0.6141 (pptt) REVERT: F 34 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8567 (mtm110) REVERT: G 5 LYS cc_start: 0.4703 (mmmt) cc_final: 0.3915 (pttp) REVERT: G 83 LEU cc_start: 0.6871 (mp) cc_final: 0.6546 (mm) REVERT: G 130 GLU cc_start: 0.5961 (tp30) cc_final: 0.5632 (tp30) REVERT: G 148 LYS cc_start: 0.7854 (mptt) cc_final: 0.7623 (mmtp) REVERT: H 78 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.7994 (mtt-85) REVERT: H 158 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7823 (mt-10) REVERT: H 234 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8286 (ttm-80) REVERT: I 438 ASN cc_start: 0.8200 (t0) cc_final: 0.7532 (t0) REVERT: I 477 ILE cc_start: 0.7812 (mm) cc_final: 0.7348 (tp) REVERT: L 451 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6432 (mtp85) REVERT: L 478 TRP cc_start: 0.8425 (t-100) cc_final: 0.8085 (t-100) REVERT: L 483 ASN cc_start: 0.8745 (m-40) cc_final: 0.8329 (m-40) REVERT: L 536 GLU cc_start: 0.8261 (tp30) cc_final: 0.8053 (tp30) REVERT: L 547 LYS cc_start: 0.8658 (tttt) cc_final: 0.8362 (ttpt) REVERT: L 577 GLU cc_start: 0.8801 (tp30) cc_final: 0.8546 (mm-30) REVERT: L 599 TYR cc_start: 0.8454 (t80) cc_final: 0.8141 (t80) REVERT: P 112 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: P 131 ASP cc_start: 0.8405 (p0) cc_final: 0.7629 (m-30) REVERT: P 169 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8034 (mm-30) outliers start: 81 outliers final: 57 residues processed: 419 average time/residue: 0.1781 time to fit residues: 115.8933 Evaluate side-chains 422 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 360 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 61 ILE 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 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 72 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 149 THR 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 85 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 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 234 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 445 CYS 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 551 GLN Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 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 460 VAL Chi-restraints excluded: chain L residue 510 HIS Chi-restraints excluded: chain L residue 554 ARG Chi-restraints excluded: chain P residue 112 GLN 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: 0.0270 chunk 295 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN E 32 GLN F 178 ASN H 203 HIS ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN J 112 GLN ** K 438 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.137378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099345 restraints weight = 38376.412| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.53 r_work: 0.3015 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26144 Z= 0.263 Angle : 0.654 15.302 35704 Z= 0.328 Chirality : 0.044 0.291 4135 Planarity : 0.004 0.048 4208 Dihedral : 15.392 175.612 4765 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.54 % Allowed : 18.57 % Favored : 77.90 % 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 are not related in a simple way. whole: -0.69 (0.15), residues: 2964 helix: 1.30 (0.16), residues: 996 sheet: -1.43 (0.20), residues: 544 loop : -1.32 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 361 TYR 0.016 0.002 TYR G 161 PHE 0.028 0.002 PHE G 14 TRP 0.015 0.002 TRP L 478 HIS 0.005 0.001 HIS P 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (26111) covalent geometry : angle 0.61028 / 0.33 (35662) hydrogen bonds : bond 0.04093 / 2.74 ( 1064) hydrogen bonds : angle 4.73299 / 3.29 ( 3100) metal coordination : bond 0.01220 / 0.80 ( 33) metal coordination : angle 6.91599 / 4.50 ( 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 446 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 359 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 87 CYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6790 (m) REVERT: A 116 GLU cc_start: 0.8873 (mp0) cc_final: 0.8645 (mp0) REVERT: A 144 PHE cc_start: 0.8315 (m-10) cc_final: 0.7842 (m-10) REVERT: A 187 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7200 (mp0) REVERT: B 22 GLU cc_start: 0.8078 (tp30) cc_final: 0.7805 (tp30) REVERT: B 116 GLU cc_start: 0.7624 (tt0) cc_final: 0.7289 (mp0) REVERT: B 123 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 196 ASP cc_start: 0.8939 (p0) cc_final: 0.8725 (p0) REVERT: D 72 ASP cc_start: 0.8456 (p0) cc_final: 0.8169 (p0) REVERT: D 152 ASN cc_start: 0.8637 (t0) cc_final: 0.8120 (t0) REVERT: E 3 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7994 (mttt) REVERT: E 150 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8794 (mm) REVERT: F 3 LYS cc_start: 0.6656 (mttt) cc_final: 0.6111 (pptt) REVERT: F 34 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8489 (mtm110) REVERT: G 5 LYS cc_start: 0.4896 (mmmt) cc_final: 0.4105 (pttp) REVERT: G 83 LEU cc_start: 0.7053 (mp) cc_final: 0.6748 (mm) REVERT: G 148 LYS cc_start: 0.7772 (mptt) cc_final: 0.7570 (mmtp) REVERT: H 31 ILE cc_start: 0.8612 (pp) cc_final: 0.8354 (pp) REVERT: H 78 ARG cc_start: 0.8555 (mtt-85) cc_final: 0.7856 (mtt-85) REVERT: H 234 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8217 (ttm-80) REVERT: H 537 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 438 ASN cc_start: 0.8161 (t0) cc_final: 0.7422 (t0) REVERT: I 477 ILE cc_start: 0.7717 (mm) cc_final: 0.7226 (tp) REVERT: J 72 ASP cc_start: 0.8351 (t70) cc_final: 0.8058 (t70) REVERT: K 116 ASP cc_start: 0.7309 (m-30) cc_final: 0.6960 (p0) REVERT: L 451 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6552 (mtp85) REVERT: L 483 ASN cc_start: 0.8741 (m-40) cc_final: 0.8305 (m-40) REVERT: L 536 GLU cc_start: 0.8224 (tp30) cc_final: 0.7966 (tp30) REVERT: L 547 LYS cc_start: 0.8626 (tttt) cc_final: 0.8315 (ttpt) REVERT: P 112 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: P 131 ASP cc_start: 0.8240 (p0) cc_final: 0.7526 (m-30) outliers start: 87 outliers final: 66 residues processed: 413 average time/residue: 0.1752 time to fit residues: 113.3301 Evaluate side-chains 420 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 349 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 ILE 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 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 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 G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ILE 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 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 439 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 445 CYS 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 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 419 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain P residue 163 SER 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: 0.6980 chunk 250 optimal weight: 0.0000 chunk 297 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 112 GLN E 32 GLN F 178 ASN ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093766 restraints weight = 38238.098| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.22 r_work: 0.3060 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26144 Z= 0.220 Angle : 0.624 15.689 35704 Z= 0.313 Chirality : 0.043 0.283 4135 Planarity : 0.004 0.041 4208 Dihedral : 15.414 176.565 4765 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.49 % Allowed : 19.14 % Favored : 77.37 % 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 are not related in a simple way. whole: -0.67 (0.15), residues: 2964 helix: 1.28 (0.16), residues: 1006 sheet: -1.45 (0.20), residues: 544 loop : -1.28 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 361 TYR 0.016 0.001 TYR G 161 PHE 0.052 0.002 PHE I 455 TRP 0.034 0.002 TRP L 478 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (26111) covalent geometry : angle 0.58041 / 0.31 (35662) hydrogen bonds : bond 0.03990 / 2.67 ( 1064) hydrogen bonds : angle 4.68047 / 3.25 ( 3100) metal coordination : bond 0.01086 / 0.72 ( 33) metal coordination : angle 6.73179 / 4.39 ( 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 453 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 367 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8112 (ttm) cc_final: 0.7767 (mtm) REVERT: A 87 CYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6879 (m) REVERT: A 116 GLU cc_start: 0.8905 (mp0) cc_final: 0.8696 (mp0) REVERT: A 144 PHE cc_start: 0.8323 (m-10) cc_final: 0.7865 (m-10) REVERT: B 22 GLU cc_start: 0.8265 (tp30) cc_final: 0.7963 (tp30) REVERT: B 116 GLU cc_start: 0.7710 (tt0) cc_final: 0.7333 (mp0) REVERT: B 123 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7093 (tm-30) REVERT: D 72 ASP cc_start: 0.8615 (p0) cc_final: 0.8344 (p0) REVERT: D 152 ASN cc_start: 0.8704 (t0) cc_final: 0.8176 (t0) REVERT: E 3 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8012 (mttt) REVERT: E 150 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8863 (mm) REVERT: F 3 LYS cc_start: 0.6673 (mttt) cc_final: 0.6123 (pptt) REVERT: F 34 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8542 (mtm110) REVERT: G 5 LYS cc_start: 0.4921 (mmmt) cc_final: 0.4112 (pttp) REVERT: G 61 PHE cc_start: 0.2596 (p90) cc_final: 0.2363 (p90) REVERT: G 83 LEU cc_start: 0.7013 (mp) cc_final: 0.6705 (mm) REVERT: G 125 GLU cc_start: 0.5781 (mm-30) cc_final: 0.5572 (mm-30) REVERT: G 148 LYS cc_start: 0.7849 (mptt) cc_final: 0.7502 (mttp) REVERT: H 78 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.7985 (mtt-85) REVERT: H 158 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7777 (mt-10) REVERT: H 234 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8298 (ttm-80) REVERT: H 537 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8226 (mm-30) REVERT: I 438 ASN cc_start: 0.8249 (t0) cc_final: 0.7544 (t0) REVERT: I 477 ILE cc_start: 0.7708 (mm) cc_final: 0.7262 (tp) REVERT: J 72 ASP cc_start: 0.8482 (t70) cc_final: 0.8189 (t70) REVERT: K 116 ASP cc_start: 0.7294 (m-30) cc_final: 0.6870 (p0) REVERT: L 451 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6644 (mtp85) REVERT: L 465 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6019 (mtp85) REVERT: L 478 TRP cc_start: 0.8743 (t-100) cc_final: 0.8224 (t-100) REVERT: L 483 ASN cc_start: 0.8770 (m-40) cc_final: 0.8331 (m-40) REVERT: L 486 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7734 (mtp85) REVERT: L 547 LYS cc_start: 0.8574 (tttt) cc_final: 0.8258 (ttpt) REVERT: P 112 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: P 123 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7225 (mt-10) REVERT: P 169 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8040 (mm-30) REVERT: P 183 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6471 (mpp-170) REVERT: P 191 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7600 (tm-30) outliers start: 86 outliers final: 67 residues processed: 419 average time/residue: 0.1714 time to fit residues: 111.1774 Evaluate side-chains 422 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 348 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 93 MET 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 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 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 188 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain 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 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 439 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 445 CYS 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 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 441 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 473 TRP Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain K residue 489 ILE Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 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 106 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 59 optimal weight: 0.8980 chunk 119 optimal weight: 0.0060 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 185 optimal weight: 0.0470 chunk 153 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 56 optimal weight: 0.0010 chunk 187 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 112 GLN E 32 GLN F 45 ASN F 178 ASN H 335 ASN ** K 438 ASN ** 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 = 0.3820 r_free = 0.3820 target = 0.140556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100486 restraints weight = 38230.137| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.48 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26144 Z= 0.109 Angle : 0.566 13.806 35704 Z= 0.288 Chirality : 0.041 0.299 4135 Planarity : 0.003 0.038 4208 Dihedral : 15.473 179.987 4765 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.13 % Allowed : 19.59 % Favored : 77.29 % 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 are not related in a simple way. whole: -0.46 (0.15), residues: 2964 helix: 1.46 (0.16), residues: 1010 sheet: -1.36 (0.21), residues: 545 loop : -1.16 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 361 TYR 0.017 0.001 TYR G 161 PHE 0.032 0.002 PHE L 538 TRP 0.036 0.001 TRP L 478 HIS 0.004 0.001 HIS K 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (26111) covalent geometry : angle 0.53392 / 0.29 (35662) hydrogen bonds : bond 0.03863 / 2.58 ( 1064) hydrogen bonds : angle 4.50721 / 3.13 ( 3100) metal coordination : bond 0.00521 / 0.33 ( 33) metal coordination : angle 5.48128 / 3.53 ( 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 457 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 380 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8119 (ttm) cc_final: 0.7738 (mtm) REVERT: A 87 CYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6978 (m) REVERT: A 93 MET cc_start: 0.8442 (tpp) cc_final: 0.8230 (mmm) REVERT: A 144 PHE cc_start: 0.8208 (m-10) cc_final: 0.7856 (m-10) REVERT: A 187 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7204 (mp0) REVERT: B 22 GLU cc_start: 0.8257 (tp30) cc_final: 0.7985 (tp30) REVERT: B 116 GLU cc_start: 0.7522 (tt0) cc_final: 0.7281 (mp0) REVERT: B 123 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 72 ASP cc_start: 0.8587 (p0) cc_final: 0.8340 (p0) REVERT: D 111 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: D 152 ASN cc_start: 0.8706 (t0) cc_final: 0.8203 (t0) REVERT: E 150 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8759 (mm) REVERT: F 3 LYS cc_start: 0.6572 (mttt) cc_final: 0.6022 (pptt) REVERT: F 34 ARG cc_start: 0.8916 (ttm-80) cc_final: 0.8510 (mtm110) REVERT: G 5 LYS cc_start: 0.4805 (mmmt) cc_final: 0.4027 (pttp) REVERT: G 83 LEU cc_start: 0.7042 (mp) cc_final: 0.6746 (mm) REVERT: G 134 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8094 (pt) REVERT: G 148 LYS cc_start: 0.7801 (mptt) cc_final: 0.7460 (mttp) REVERT: H 31 ILE cc_start: 0.8669 (pp) cc_final: 0.8401 (pp) REVERT: H 78 ARG cc_start: 0.8734 (mtt-85) cc_final: 0.7989 (mtt-85) REVERT: H 158 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7776 (mt-10) REVERT: H 234 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8152 (ttm-80) REVERT: H 361 ARG cc_start: 0.7691 (mtp-110) cc_final: 0.7195 (ptm160) REVERT: I 438 ASN cc_start: 0.8201 (t0) cc_final: 0.7494 (t0) REVERT: I 453 MET cc_start: 0.8378 (ttt) cc_final: 0.8085 (ttt) REVERT: I 477 ILE cc_start: 0.7741 (mm) cc_final: 0.7301 (tp) REVERT: I 485 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6523 (mmp) REVERT: I 551 GLN cc_start: 0.8650 (tt0) cc_final: 0.8337 (tm-30) REVERT: J 196 ASP cc_start: 0.8501 (p0) cc_final: 0.8287 (p0) REVERT: K 116 ASP cc_start: 0.7427 (m-30) cc_final: 0.6981 (p0) REVERT: L 451 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6482 (mtp85) REVERT: L 465 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6060 (mtp85) REVERT: L 483 ASN cc_start: 0.8770 (m-40) cc_final: 0.8358 (m-40) REVERT: L 486 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7651 (mtp85) REVERT: L 533 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7927 (mt-10) REVERT: L 547 LYS cc_start: 0.8481 (tttt) cc_final: 0.8181 (ttpt) REVERT: L 577 GLU cc_start: 0.8870 (tp30) cc_final: 0.8648 (mm-30) REVERT: P 112 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: P 131 ASP cc_start: 0.8087 (p0) cc_final: 0.7246 (m-30) REVERT: P 169 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8050 (mm-30) REVERT: P 183 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6368 (mpp-170) outliers start: 77 outliers final: 51 residues processed: 426 average time/residue: 0.1771 time to fit residues: 118.2691 Evaluate side-chains 419 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 359 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS 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 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 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 441 THR Chi-restraints excluded: chain I residue 445 CYS 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 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 441 THR 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 106 SER Chi-restraints excluded: chain P residue 112 GLN 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: 6.9990 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN E 32 GLN F 154 GLN F 178 ASN ** K 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097680 restraints weight = 38247.835| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.53 r_work: 0.3068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26144 Z= 0.186 Angle : 0.603 13.796 35704 Z= 0.303 Chirality : 0.043 0.290 4135 Planarity : 0.004 0.040 4208 Dihedral : 15.341 177.675 4765 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.72 % Allowed : 20.24 % Favored : 77.04 % 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 are not related in a simple way. whole: -0.44 (0.15), residues: 2964 helix: 1.46 (0.16), residues: 1010 sheet: -1.30 (0.21), residues: 535 loop : -1.15 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 361 TYR 0.016 0.001 TYR G 161 PHE 0.027 0.002 PHE L 538 TRP 0.019 0.002 TRP L 535 HIS 0.005 0.001 HIS K 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (26111) covalent geometry : angle 0.56719 / 0.30 (35662) hydrogen bonds : bond 0.03818 / 2.55 ( 1064) hydrogen bonds : angle 4.51056 / 3.13 ( 3100) metal coordination : bond 0.00835 / 0.55 ( 33) metal coordination : angle 5.97069 / 3.86 ( 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 430 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 363 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8141 (ttm) cc_final: 0.7808 (mtm) REVERT: A 87 CYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6977 (m) REVERT: A 93 MET cc_start: 0.8565 (tpp) cc_final: 0.8365 (mmm) REVERT: B 9 TYR cc_start: 0.8664 (m-80) cc_final: 0.8445 (m-80) REVERT: B 22 GLU cc_start: 0.8272 (tp30) cc_final: 0.7993 (tp30) REVERT: B 116 GLU cc_start: 0.7671 (tt0) cc_final: 0.7373 (mp0) REVERT: B 123 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7031 (tm-30) REVERT: D 72 ASP cc_start: 0.8636 (p0) cc_final: 0.8392 (p0) REVERT: D 152 ASN cc_start: 0.8755 (t0) cc_final: 0.8220 (t0) REVERT: E 150 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8858 (mm) REVERT: F 3 LYS cc_start: 0.6695 (mttt) cc_final: 0.6184 (pptt) REVERT: G 5 LYS cc_start: 0.4929 (mmmt) cc_final: 0.4081 (pttp) REVERT: G 83 LEU cc_start: 0.7113 (mp) cc_final: 0.6818 (mm) REVERT: G 134 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8077 (pt) REVERT: G 148 LYS cc_start: 0.7803 (mptt) cc_final: 0.7482 (mttp) REVERT: H 31 ILE cc_start: 0.8760 (pp) cc_final: 0.8476 (pp) REVERT: H 78 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.8071 (mtt-85) REVERT: H 158 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7821 (mt-10) REVERT: H 234 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (ttm-80) REVERT: H 361 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.7171 (ptm160) REVERT: I 438 ASN cc_start: 0.8247 (t0) cc_final: 0.7593 (t0) REVERT: I 477 ILE cc_start: 0.7744 (mm) cc_final: 0.7310 (tp) REVERT: I 485 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6626 (mmp) REVERT: I 551 GLN cc_start: 0.8679 (tt0) cc_final: 0.8407 (tm-30) REVERT: J 72 ASP cc_start: 0.8391 (t70) cc_final: 0.8130 (t70) REVERT: K 116 ASP cc_start: 0.7391 (m-30) cc_final: 0.6979 (p0) REVERT: K 145 ASN cc_start: 0.8093 (p0) cc_final: 0.7846 (p0) REVERT: L 451 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6516 (mtp85) REVERT: L 465 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6109 (mtp85) REVERT: L 478 TRP cc_start: 0.8542 (t-100) cc_final: 0.8127 (t-100) REVERT: L 483 ASN cc_start: 0.8731 (m-40) cc_final: 0.8297 (m-40) REVERT: L 486 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7688 (mtp85) REVERT: L 547 LYS cc_start: 0.8523 (tttt) cc_final: 0.8207 (ttpt) REVERT: L 577 GLU cc_start: 0.8866 (tp30) cc_final: 0.8642 (mm-30) REVERT: P 112 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: P 131 ASP cc_start: 0.8094 (p0) cc_final: 0.7293 (m-30) REVERT: P 169 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8105 (mm-30) REVERT: P 183 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6505 (mpp-170) outliers start: 67 outliers final: 53 residues processed: 405 average time/residue: 0.1721 time to fit residues: 108.3811 Evaluate side-chains 416 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 CYS 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 44 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 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 441 THR Chi-restraints excluded: chain I residue 476 MET Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain 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 441 THR 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 106 SER Chi-restraints excluded: chain P residue 112 GLN 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: 1.9990 chunk 175 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN F 45 ASN F 154 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.140593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097476 restraints weight = 38177.343| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26144 Z= 0.131 Angle : 0.574 13.474 35704 Z= 0.290 Chirality : 0.041 0.291 4135 Planarity : 0.003 0.039 4208 Dihedral : 15.359 178.800 4765 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.80 % Allowed : 20.07 % Favored : 77.12 % 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 are not related in a simple way. whole: -0.35 (0.15), residues: 2964 helix: 1.56 (0.16), residues: 1008 sheet: -1.28 (0.21), residues: 536 loop : -1.11 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 361 TYR 0.021 0.001 TYR G 38 PHE 0.025 0.001 PHE L 538 TRP 0.020 0.001 TRP L 478 HIS 0.004 0.001 HIS K 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26111) covalent geometry : angle 0.54110 / 0.29 (35662) hydrogen bonds : bond 0.03744 / 2.51 ( 1064) hydrogen bonds : angle 4.44169 / 3.09 ( 3100) metal coordination : bond 0.00634 / 0.42 ( 33) metal coordination : angle 5.56972 / 3.59 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.54 seconds wall clock time: 114 minutes 27.00 seconds (6867.00 seconds total)