Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 13:33:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exv_3981/07_2023/6exv_3981_neut_updated.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 198 5.16 5 C 20415 2.51 5 N 5741 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 770": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 32717 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11317 Classifications: {'peptide': 1428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1357} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'CSX:plan-1': 1, 'HYP:plan-1': 1, 'ILX:plan-1': 1, 'TRX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 301 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 735 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 38.847 79.318 106.425 1.00 46.90 S ATOM 486 SG CYS A 74 39.588 84.008 106.933 1.00 45.60 S ATOM 533 SG CYS A 81 40.493 82.266 103.879 1.00 40.48 S ATOM 768 SG CYS A 111 85.660 74.861 121.372 1.00 62.21 S ATOM 796 SG CYS A 114 83.602 76.125 125.393 1.00 63.39 S ATOM 1109 SG CYS A 154 87.890 76.877 123.396 1.00 79.56 S ATOM 19949 SG CYS B1119 50.272 92.971 114.828 1.00 41.50 S ATOM 19971 SG CYS B1122 53.286 90.175 114.329 1.00 44.44 S ATOM 21086 SG CYS C 90 7.666 94.273 47.343 1.00 89.17 S ATOM 21121 SG CYS C 94 7.713 93.531 43.872 1.00 72.28 S ATOM 28949 SG CYS I 86 113.084 63.272 33.301 1.00 50.23 S ATOM 28973 SG CYS I 89 111.906 60.705 30.947 1.00 47.04 S ATOM 29177 SG CYS I 114 109.064 61.928 33.056 1.00 35.97 S ATOM 29212 SG CYS I 119 112.031 59.124 34.218 1.00 56.27 S ATOM 29346 SG CYS J 10 39.833 92.625 29.744 1.00 28.61 S ATOM 29610 SG CYS J 44 43.220 91.743 29.910 1.00 27.15 S ATOM 29616 SG CYS J 45 39.743 88.835 28.240 1.00 27.63 S ATOM 30762 SG CYS L 19 27.685 51.436 54.616 1.00 39.64 S ATOM 30781 SG CYS L 22 25.775 49.259 51.422 1.00 42.62 S ATOM 30898 SG CYS L 36 24.598 49.251 55.501 1.00 56.26 S ATOM 30924 SG CYS L 39 27.603 47.584 54.190 1.00 58.02 S Time building chain proxies: 15.53, per 1000 atoms: 0.47 Number of scatterers: 32717 At special positions: 0 Unit cell: (156.22, 172.27, 171.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 198 16.00 P 75 15.00 Mg 1 11.99 O 6279 8.00 N 5741 7.00 C 20415 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.18 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 15 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 37 sheets defined 27.9% alpha, 10.1% beta 26 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 11.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.058A pdb=" N LEU A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL A 101 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 102 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 137 through 148 removed outlier: 4.096A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 4.451A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 245 through 248 removed outlier: 3.517A pdb=" N MET A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.965A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 4.051A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.837A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.125A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 4.284A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 663 through 683 removed outlier: 3.921A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 698 through 721 Processing helix chain 'A' and resid 733 through 747 Processing helix chain 'A' and resid 750 through 759 removed outlier: 3.840A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 778 through 785 removed outlier: 3.818A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 867 removed outlier: 4.688A pdb=" N PHE A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.764A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 936 through 942 removed outlier: 4.388A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 951 Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.956A pdb=" N GLU A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 993 removed outlier: 3.862A pdb=" N ALA A 990 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1018 removed outlier: 4.169A pdb=" N GLU A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1037 Processing helix chain 'A' and resid 1040 through 1048 Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1063 through 1076 removed outlier: 3.832A pdb=" N TRP A1067 " --> pdb=" O GLU A1063 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1090 No H-bonds generated for 'chain 'A' and resid 1087 through 1090' Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1121 through 1127 Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 Processing helix chain 'A' and resid 1190 through 1198 Processing helix chain 'A' and resid 1218 through 1222 Processing helix chain 'A' and resid 1228 through 1234 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1281 through 1292 Processing helix chain 'A' and resid 1343 through 1347 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1372 through 1388 removed outlier: 3.931A pdb=" N PHE A1388 " --> pdb=" O HIS A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1429 No H-bonds generated for 'chain 'A' and resid 1426 through 1429' Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'B' and resid 22 through 36 removed outlier: 4.137A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 3.612A pdb=" N MET B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 removed outlier: 3.596A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.875A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 359 through 376 Processing helix chain 'B' and resid 396 through 421 removed outlier: 4.550A pdb=" N PHE B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 538 through 548 removed outlier: 4.080A pdb=" N LEU B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 727 removed outlier: 3.776A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 removed outlier: 4.356A pdb=" N ARG B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 970 through 973 No H-bonds generated for 'chain 'B' and resid 970 through 973' Processing helix chain 'B' and resid 979 through 993 removed outlier: 3.975A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1015 Processing helix chain 'B' and resid 1092 through 1095 No H-bonds generated for 'chain 'B' and resid 1092 through 1095' Processing helix chain 'B' and resid 1101 through 1107 Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 4.504A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 244 through 268 Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 85 through 97 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'G' and resid 25 through 32 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.709A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.738A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 removed outlier: 4.029A pdb=" N LEU J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 45 No H-bonds generated for 'chain 'J' and resid 43 through 45' Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 56 through 59 No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.180A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.707A pdb=" N GLY A 86 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 198 through 200 removed outlier: 4.295A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.757A pdb=" N MET A 266 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.840A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.311A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 378 through 380 Processing sheet with id= G, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= H, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= I, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= J, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 4.478A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= L, first strand: chain 'B' and resid 83 through 88 Processing sheet with id= M, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.054A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= O, first strand: chain 'B' and resid 602 through 606 removed outlier: 3.684A pdb=" N ASP B 606 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 622 through 626 Processing sheet with id= Q, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.551A pdb=" N GLU B 816 " --> pdb=" O CYS B 919 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.352A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 947 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= T, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= U, first strand: chain 'B' and resid 565 through 569 removed outlier: 3.651A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.522A pdb=" N ALA C 46 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.642A pdb=" N ALA C 54 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.640A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 182 through 185 Processing sheet with id= Z, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.617A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.516A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.668A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AD, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.797A pdb=" N TYR G 3 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 71 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN G 53 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 85 through 87 removed outlier: 4.018A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 104 through 108 removed outlier: 5.331A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.425A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 113 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 56 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.825A pdb=" N LEU I 36 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 94 through 97 Processing sheet with id= AJ, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.820A pdb=" N ASN K 22 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU K 32 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 25 through 27 779 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 12.22 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5409 1.31 - 1.44: 8831 1.44 - 1.57: 18789 1.57 - 1.70: 147 1.70 - 1.83: 313 Bond restraints: 33489 Sorted by residual: bond pdb=" CA ILX M 1 " pdb=" C ILX M 1 " ideal model delta sigma weight residual 1.529 1.475 0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" C HYP M 8 " pdb=" O HYP M 8 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" CG LEU A 585 " pdb=" CD1 LEU A 585 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CG GLN A 790 " pdb=" CD GLN A 790 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.55e+00 bond pdb=" CB ASP K 80 " pdb=" CG ASP K 80 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.55e+00 ... (remaining 33484 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.70: 1127 105.70 - 114.13: 19265 114.13 - 122.57: 20528 122.57 - 131.00: 4493 131.00 - 139.43: 153 Bond angle restraints: 45566 Sorted by residual: angle pdb=" C LYS A 812 " pdb=" N ASP A 813 " pdb=" CA ASP A 813 " ideal model delta sigma weight residual 122.82 130.95 -8.13 1.42e+00 4.96e-01 3.28e+01 angle pdb=" N GLY B1087 " pdb=" CA GLY B1087 " pdb=" C GLY B1087 " ideal model delta sigma weight residual 113.18 126.24 -13.06 2.37e+00 1.78e-01 3.04e+01 angle pdb=" C SER A 530 " pdb=" N ASN A 531 " pdb=" CA ASN A 531 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C GLY B 862 " pdb=" N ASP B 863 " pdb=" CA ASP B 863 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" N SER A 480 " pdb=" CA SER A 480 " pdb=" C SER A 480 " ideal model delta sigma weight residual 111.30 118.09 -6.79 1.43e+00 4.89e-01 2.25e+01 ... (remaining 45561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 19873 34.63 - 69.25: 358 69.25 - 103.88: 14 103.88 - 138.50: 0 138.50 - 173.13: 3 Dihedral angle restraints: 20248 sinusoidal: 8888 harmonic: 11360 Sorted by residual: dihedral pdb=" CA ARG E 54 " pdb=" C ARG E 54 " pdb=" N ARG E 55 " pdb=" CA ARG E 55 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 149.75 30.25 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA GLU B1088 " pdb=" C GLU B1088 " pdb=" N MET B1089 " pdb=" CA MET B1089 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 20245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4160 0.080 - 0.159: 841 0.159 - 0.239: 90 0.239 - 0.318: 9 0.318 - 0.398: 2 Chirality restraints: 5102 Sorted by residual: chirality pdb=" CB ILE G 101 " pdb=" CA ILE G 101 " pdb=" CG1 ILE G 101 " pdb=" CG2 ILE G 101 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA HYP M 8 " pdb=" N HYP M 8 " pdb=" C HYP M 8 " pdb=" CB HYP M 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' A P 12 " pdb=" C4' A P 12 " pdb=" O3' A P 12 " pdb=" C2' A P 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5099 not shown) Planarity restraints: 5645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 573 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP B 573 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 573 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 573 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 573 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 573 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 573 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 573 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1029 " 0.020 2.00e-02 2.50e+03 2.11e-02 8.91e+00 pdb=" CG TYR B1029 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B1029 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B1029 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B1029 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B1029 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B1029 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B1029 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " 0.022 2.00e-02 2.50e+03 2.09e-02 8.74e+00 pdb=" CG TYR B1048 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " 0.002 2.00e-02 2.50e+03 ... (remaining 5642 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 219 2.60 - 3.17: 25281 3.17 - 3.75: 47033 3.75 - 4.32: 66832 4.32 - 4.90: 110998 Nonbonded interactions: 250363 Sorted by model distance: nonbonded pdb=" NH2 ARG B 591 " pdb=" OE2 GLU B 663 " model vdw 2.022 2.520 nonbonded pdb=" O3' C P 20 " pdb="MG MG A2003 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.065 2.170 nonbonded pdb=" OD2 ASP H 71 " pdb=" OH TYR H 142 " model vdw 2.075 2.440 nonbonded pdb=" O ASN I 22 " pdb="ZN ZN I 201 " model vdw 2.110 2.230 ... (remaining 250358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.870 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 88.880 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.100 33489 Z= 0.549 Angle : 1.096 16.269 45566 Z= 0.592 Chirality : 0.064 0.398 5102 Planarity : 0.007 0.069 5645 Dihedral : 12.805 173.126 12900 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.86 % Favored : 91.09 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.11), residues: 3860 helix: -3.83 (0.09), residues: 1187 sheet: -1.82 (0.21), residues: 535 loop : -3.02 (0.11), residues: 2138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 610 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 619 average time/residue: 0.5055 time to fit residues: 479.3206 Evaluate side-chains 420 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 3.484 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2821 time to fit residues: 6.1577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 50.0000 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 226 optimal weight: 0.0670 chunk 353 optimal weight: 10.0000 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 576 GLN A 671 ASN A 673 GLN A 678 ASN A1163 HIS A1230 GLN B 518 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 649 ASN B 741 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 941 GLN B 992 ASN C 190 ASN G 14 HIS G 139 GLN H 46 GLN I 22 ASN I 41 ASN I 121 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 33489 Z= 0.166 Angle : 0.591 11.291 45566 Z= 0.307 Chirality : 0.044 0.208 5102 Planarity : 0.005 0.059 5645 Dihedral : 12.981 173.386 5037 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 3860 helix: -2.20 (0.13), residues: 1186 sheet: -1.37 (0.21), residues: 537 loop : -2.62 (0.12), residues: 2137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 493 time to evaluate : 3.778 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 516 average time/residue: 0.4802 time to fit residues: 394.4498 Evaluate side-chains 426 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 413 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2832 time to fit residues: 11.8220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 353 optimal weight: 0.5980 chunk 382 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 350 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 283 optimal weight: 30.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 741 HIS B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS B1021 HIS B1120 ASN C 66 HIS C 260 GLN D 34 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 67 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 33489 Z= 0.275 Angle : 0.630 10.948 45566 Z= 0.325 Chirality : 0.046 0.199 5102 Planarity : 0.005 0.051 5645 Dihedral : 12.809 174.015 5037 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.12), residues: 3860 helix: -1.53 (0.14), residues: 1191 sheet: -1.09 (0.22), residues: 556 loop : -2.40 (0.12), residues: 2113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 433 time to evaluate : 3.765 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 34 residues processed: 480 average time/residue: 0.4944 time to fit residues: 376.3684 Evaluate side-chains 443 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 409 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3264 time to fit residues: 25.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 355 optimal weight: 10.0000 chunk 376 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN A1005 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 825 GLN B 941 GLN C 260 GLN E 210 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 67 GLN J 61 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.139 33489 Z= 0.527 Angle : 0.775 12.162 45566 Z= 0.397 Chirality : 0.052 0.203 5102 Planarity : 0.006 0.058 5645 Dihedral : 13.054 173.463 5037 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.96 % Favored : 91.01 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 3860 helix: -1.60 (0.14), residues: 1213 sheet: -1.14 (0.22), residues: 540 loop : -2.45 (0.12), residues: 2107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 426 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 39 residues processed: 476 average time/residue: 0.4915 time to fit residues: 372.8744 Evaluate side-chains 442 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 403 time to evaluate : 3.607 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3024 time to fit residues: 27.5606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 320 optimal weight: 40.0000 chunk 259 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 337 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN B 144 HIS B 456 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN E 168 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 33489 Z= 0.153 Angle : 0.555 10.980 45566 Z= 0.286 Chirality : 0.044 0.189 5102 Planarity : 0.004 0.055 5645 Dihedral : 12.754 175.960 5037 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.13), residues: 3860 helix: -0.82 (0.15), residues: 1189 sheet: -0.82 (0.23), residues: 522 loop : -2.15 (0.13), residues: 2149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 439 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 470 average time/residue: 0.4846 time to fit residues: 360.4417 Evaluate side-chains 417 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 403 time to evaluate : 3.599 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3531 time to fit residues: 13.7201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 0.5980 chunk 338 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 312 optimal weight: 0.0570 chunk 174 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 941 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 33489 Z= 0.213 Angle : 0.573 10.728 45566 Z= 0.293 Chirality : 0.045 0.194 5102 Planarity : 0.004 0.051 5645 Dihedral : 12.699 176.406 5037 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 3860 helix: -0.58 (0.15), residues: 1183 sheet: -0.65 (0.22), residues: 560 loop : -2.07 (0.13), residues: 2117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 418 time to evaluate : 3.889 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 448 average time/residue: 0.4828 time to fit residues: 344.0390 Evaluate side-chains 420 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 401 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3506 time to fit residues: 18.6990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 274 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 234 optimal weight: 0.1980 chunk 228 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN B 518 HIS B 941 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 33489 Z= 0.243 Angle : 0.589 10.830 45566 Z= 0.301 Chirality : 0.045 0.195 5102 Planarity : 0.004 0.052 5645 Dihedral : 12.724 177.683 5037 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 3860 helix: -0.52 (0.15), residues: 1189 sheet: -0.62 (0.22), residues: 560 loop : -2.02 (0.13), residues: 2111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 410 time to evaluate : 3.846 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 440 average time/residue: 0.4834 time to fit residues: 336.6688 Evaluate side-chains 418 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 398 time to evaluate : 3.577 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3194 time to fit residues: 16.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN B 518 HIS B 941 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 41 ASN I 67 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 33489 Z= 0.379 Angle : 0.670 11.418 45566 Z= 0.342 Chirality : 0.048 0.194 5102 Planarity : 0.005 0.051 5645 Dihedral : 12.858 179.065 5037 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3860 helix: -0.73 (0.15), residues: 1193 sheet: -0.72 (0.22), residues: 581 loop : -2.07 (0.13), residues: 2086 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 405 time to evaluate : 3.571 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 414 average time/residue: 0.4928 time to fit residues: 323.8119 Evaluate side-chains 405 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 394 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2966 time to fit residues: 11.3644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 327 optimal weight: 8.9990 chunk 349 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 330 optimal weight: 9.9990 chunk 348 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 33489 Z= 0.156 Angle : 0.543 11.548 45566 Z= 0.279 Chirality : 0.044 0.194 5102 Planarity : 0.004 0.053 5645 Dihedral : 12.687 177.789 5037 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3860 helix: -0.28 (0.15), residues: 1182 sheet: -0.47 (0.23), residues: 554 loop : -1.88 (0.13), residues: 2124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 408 time to evaluate : 3.605 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 419 average time/residue: 0.4970 time to fit residues: 329.9264 Evaluate side-chains 401 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 394 time to evaluate : 3.456 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4091 time to fit residues: 9.6013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 10.0000 chunk 369 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 387 optimal weight: 10.0000 chunk 356 optimal weight: 0.5980 chunk 308 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 238 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 33489 Z= 0.168 Angle : 0.549 11.431 45566 Z= 0.279 Chirality : 0.044 0.198 5102 Planarity : 0.004 0.052 5645 Dihedral : 12.609 175.519 5037 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3860 helix: -0.10 (0.16), residues: 1192 sheet: -0.37 (0.23), residues: 550 loop : -1.78 (0.13), residues: 2118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 406 time to evaluate : 3.581 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 410 average time/residue: 0.5093 time to fit residues: 332.3761 Evaluate side-chains 395 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 3.331 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3236 time to fit residues: 5.9929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 0.8980 chunk 328 optimal weight: 50.0000 chunk 94 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 309 optimal weight: 0.0670 chunk 129 optimal weight: 10.0000 chunk 317 optimal weight: 0.0170 chunk 39 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.173009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136527 restraints weight = 34664.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134095 restraints weight = 38966.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133896 restraints weight = 38984.816| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 33489 Z= 0.203 Angle : 0.566 11.366 45566 Z= 0.288 Chirality : 0.044 0.196 5102 Planarity : 0.004 0.051 5645 Dihedral : 12.624 173.601 5037 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3860 helix: -0.09 (0.15), residues: 1193 sheet: -0.33 (0.23), residues: 557 loop : -1.76 (0.13), residues: 2110 =============================================================================== Job complete usr+sys time: 6704.99 seconds wall clock time: 122 minutes 43.86 seconds (7363.86 seconds total)