Starting phenix.real_space_refine on Thu Sep 26 23:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/09_2024/8dy9_27778.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 1.038 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: 9 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 143 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 19778 2.51 5 N 5779 2.21 5 O 6473 1.98 5 H 31140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63435 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3519 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4908 Classifications: {'peptide': 319} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Chain: "C" Number of atoms: 17368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 17368 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1060} Chain: "D" Number of atoms: 19789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 19789 Classifications: {'peptide': 1253} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1199} Chain breaks: 1 Chain: "E" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1202 Classifications: {'peptide': 77} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4873 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "G" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1657 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1158 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4496 Classifications: {'peptide': 303} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 291} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "O" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1197 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "P" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1209 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1096 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "R" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 951 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "D" 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: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" 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 39972 SG CYS D 886 17.847 115.009 90.208 1.00 63.78 S ATOM 41111 SG CYS D 962 21.461 114.786 91.466 1.00 62.70 S ATOM 41194 SG CYS D 969 20.288 113.014 88.150 1.00 57.34 S ATOM 41234 SG CYS D 972 20.757 116.591 88.248 1.00 56.95 S ATOM 26743 SG CYS D 60 53.484 64.128 118.695 1.00 87.50 S ATOM 26774 SG CYS D 62 55.402 63.067 121.730 1.00 89.25 S ATOM 27007 SG CYS D 75 51.645 63.071 121.890 1.00 98.05 S ATOM 27056 SG CYS D 78 53.471 66.335 121.941 1.00 91.51 S ATOM 53526 SG CYS H 25 57.965 45.973 75.138 1.00 56.96 S ATOM 53866 SG CYS H 48 59.855 40.076 73.728 1.00 67.31 S ATOM 53996 SG CYS H 57 63.574 43.661 77.464 1.00 74.97 S ATOM 53905 SG CYS H 51 62.764 45.469 71.249 1.00 65.27 S ATOM 54753 SG CYS I 18 39.499 59.797 75.697 1.00 53.83 S ATOM 54763 SG CYS I 19 36.581 57.926 73.672 1.00 49.15 S ATOM 56286 SG CYS I 122 37.297 56.595 77.111 1.00 47.39 S Time building chain proxies: 21.51, per 1000 atoms: 0.34 Number of scatterers: 63435 At special positions: 0 Unit cell: (128.877, 172.197, 200.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 114 16.00 P 143 15.00 Mg 1 11.99 O 6473 8.00 N 5779 7.00 C 19778 6.00 H 31140 1.00 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: 12.56 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 H 101 " pdb="FE1 SF4 H 101 " - pdb=" SG CYS H 25 " pdb="FE2 SF4 H 101 " - pdb=" SG CYS H 48 " pdb="FE4 SF4 H 101 " - pdb=" SG CYS H 51 " pdb="FE3 SF4 H 101 " - pdb=" SG CYS H 57 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 972 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 886 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 969 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 962 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 122 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 18 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 19 " Number of angles added : 12 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6958 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 43 sheets defined 44.0% alpha, 14.0% beta 66 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 21.63 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 4.096A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.560A pdb=" N ILE A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.027A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.835A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 257 through 266 removed outlier: 3.785A pdb=" N ARG B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.870A pdb=" N LEU B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.590A pdb=" N ASP B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.909A pdb=" N GLU B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 removed outlier: 4.352A pdb=" N SER C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.545A pdb=" N LEU C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.665A pdb=" N ARG C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 314 through 326 Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 383 through 410 removed outlier: 3.637A pdb=" N ARG C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 535 through 542 Processing helix chain 'C' and resid 593 through 597 removed outlier: 3.650A pdb=" N MET C 596 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 597 " --> pdb=" O THR C 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 593 through 597' Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 604 through 615 Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 780 through 786 removed outlier: 3.535A pdb=" N ALA C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP C 786 " --> pdb=" O VAL C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 859 through 861 No H-bonds generated for 'chain 'C' and resid 859 through 861' Processing helix chain 'C' and resid 923 through 929 removed outlier: 4.410A pdb=" N SER C 927 " --> pdb=" O LEU C 923 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 928 " --> pdb=" O GLY C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 946 Processing helix chain 'C' and resid 954 through 962 removed outlier: 3.836A pdb=" N ARG C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 960 " --> pdb=" O TRP C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 991 Processing helix chain 'C' and resid 1071 through 1082 Processing helix chain 'C' and resid 1083 through 1092 removed outlier: 3.882A pdb=" N LEU C1087 " --> pdb=" O ALA C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1111 removed outlier: 4.315A pdb=" N VAL C1102 " --> pdb=" O VAL C1098 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C1103 " --> pdb=" O THR C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1133 removed outlier: 3.842A pdb=" N LYS C1124 " --> pdb=" O PRO C1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.671A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 184 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 190 through 228 removed outlier: 5.027A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.733A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.556A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.145A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 3.581A pdb=" N ASP D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.640A pdb=" N ASN D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 606 through 616 removed outlier: 3.521A pdb=" N ALA D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.525A pdb=" N ALA D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 721 Processing helix chain 'D' and resid 736 through 758 removed outlier: 3.549A pdb=" N ILE D 740 " --> pdb=" O ALA D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 813 removed outlier: 3.744A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.882A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 Processing helix chain 'D' and resid 988 through 999 Processing helix chain 'D' and resid 1000 through 1004 Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.628A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLN D1110 " --> pdb=" O ARG D1106 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N ARG D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA D1112 " --> pdb=" O LEU D1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.133A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1178 removed outlier: 3.689A pdb=" N THR D1178 " --> pdb=" O ARG D1174 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1210 Processing helix chain 'D' and resid 1211 through 1223 removed outlier: 3.743A pdb=" N ILE D1221 " --> pdb=" O THR D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1238 removed outlier: 4.070A pdb=" N ASN D1234 " --> pdb=" O GLY D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1247 removed outlier: 3.771A pdb=" N LEU D1247 " --> pdb=" O GLY D1244 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.547A pdb=" N ALA D1264 " --> pdb=" O GLU D1260 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET D1265 " --> pdb=" O ALA D1261 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.534A pdb=" N GLU E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 46 removed outlier: 3.601A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 217 through 227 removed outlier: 3.543A pdb=" N GLY F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 256 Processing helix chain 'F' and resid 261 through 297 removed outlier: 4.958A pdb=" N ARG F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 321 Processing helix chain 'F' and resid 329 through 350 removed outlier: 4.440A pdb=" N TYR F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 378 Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 404 removed outlier: 3.541A pdb=" N GLY F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 454 removed outlier: 3.689A pdb=" N THR F 453 " --> pdb=" O SER F 449 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 454 " --> pdb=" O VAL F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 467 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 486 through 502 Processing helix chain 'F' and resid 507 through 512 removed outlier: 4.574A pdb=" N ASP F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 91 through 108 Processing helix chain 'H' and resid 19 through 28 removed outlier: 6.497A pdb=" N LEU H 24 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.733A pdb=" N PHE H 33 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 49 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 75 through 85 removed outlier: 4.191A pdb=" N ALA H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 51 through 65 Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.764A pdb=" N GLY I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 135 Processing helix chain 'I' and resid 153 through 167 removed outlier: 3.505A pdb=" N LEU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 198 removed outlier: 3.760A pdb=" N GLY I 198 " --> pdb=" O LEU I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 215 removed outlier: 3.616A pdb=" N VAL I 215 " --> pdb=" O MET I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 256 through 269 Processing helix chain 'I' and resid 273 through 280 Processing helix chain 'I' and resid 286 through 301 removed outlier: 3.532A pdb=" N VAL I 290 " --> pdb=" O THR I 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.470A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.969A pdb=" N TYR A 96 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.762A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.516A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 22 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.229A pdb=" N TYR B 96 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.475A pdb=" N ILE C 40 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 5.371A pdb=" N LEU C 110 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR C 145 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 112 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU C 143 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 114 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR C 141 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA C 136 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C 161 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 138 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 382 removed outlier: 3.586A pdb=" N SER C 182 " --> pdb=" O ARG C 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 196 removed outlier: 3.689A pdb=" N LEU C 217 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB8, first strand: chain 'C' and resid 508 through 509 removed outlier: 4.976A pdb=" N GLU C 530 " --> pdb=" O LYS C 521 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL C 523 " --> pdb=" O THR C 528 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR C 528 " --> pdb=" O VAL C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 565 Processing sheet with id=AC2, first strand: chain 'C' and resid 645 through 646 removed outlier: 6.794A pdb=" N LEU C 645 " --> pdb=" O LEU C 705 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 670 through 674 removed outlier: 5.943A pdb=" N ALA C 664 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 653 " --> pdb=" O ALA C 664 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 679 through 680 Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.759A pdb=" N GLU C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1009 through 1010 removed outlier: 6.847A pdb=" N ILE C 738 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE C 901 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 740 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 739 " --> pdb=" O ILE C 919 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE C 918 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 723 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU C 920 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA C 725 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C1026 " --> pdb=" O PHE C 726 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 6.979A pdb=" N ASP C 764 " --> pdb=" O VAL C 868 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL C 868 " --> pdb=" O ASP C 764 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASN C 869 " --> pdb=" O ASP C 857 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP C 857 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 871 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C 855 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG C 873 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 853 " --> pdb=" O ARG C 873 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR C 875 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS C 879 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ILE C 847 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 848 " --> pdb=" O VAL C 799 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 771 through 772 Processing sheet with id=AC9, first strand: chain 'C' and resid 804 through 806 removed outlier: 6.564A pdb=" N LEU C 840 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 947 through 948 Processing sheet with id=AD2, first strand: chain 'C' and resid 1044 through 1046 Processing sheet with id=AD3, first strand: chain 'C' and resid 1069 through 1070 Processing sheet with id=AD4, first strand: chain 'C' and resid 1138 through 1140 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.220A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ALA D 99 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.682A pdb=" N GLU D 235 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 408 through 409 removed outlier: 6.296A pdb=" N PHE D 335 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY G 8 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD9, first strand: chain 'D' and resid 892 through 895 removed outlier: 4.708A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 924 through 926 removed outlier: 7.132A pdb=" N VAL D 924 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1070 through 1074 removed outlier: 3.533A pdb=" N THR D1056 " --> pdb=" O THR D1053 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D1053 " --> pdb=" O THR D1056 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D1058 " --> pdb=" O GLU D1051 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.830A pdb=" N ARG D1147 " --> pdb=" O GLN D1189 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.600A pdb=" N ARG D1254 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.818A pdb=" N ALA G 33 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU G 64 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 32 through 34 Processing sheet with id=AE7, first strand: chain 'I' and resid 172 through 176 1360 hydrogen bonds defined for protein. 3849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 24.30 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 31127 1.13 - 1.41: 13184 1.41 - 1.70: 19735 1.70 - 1.99: 192 1.99 - 2.28: 12 Bond restraints: 64250 Sorted by residual: bond pdb=" N4 DC Q 12 " pdb=" H42 DC Q 12 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" N4 DC Q 12 " pdb=" H41 DC Q 12 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" C5 DC Q 12 " pdb=" H5 DC Q 12 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC Q 12 " pdb=" H6 DC Q 12 " ideal model delta sigma weight residual 0.930 1.077 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C3' DC Q 12 " pdb=" H3' DC Q 12 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 64245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 116502 7.08 - 14.15: 3 14.15 - 21.23: 2 21.23 - 28.30: 0 28.30 - 35.38: 3 Bond angle restraints: 116510 Sorted by residual: angle pdb=" C LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 109.00 74.06 34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 110.00 77.99 32.01 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C3' DC Q 21 " pdb=" O3' DC Q 21 " pdb=" P DG Q 22 " ideal model delta sigma weight residual 120.20 104.38 15.82 1.50e+00 4.44e-01 1.11e+02 angle pdb=" C3' DT Q 16 " pdb=" O3' DT Q 16 " pdb=" P DC Q 17 " ideal model delta sigma weight residual 120.20 104.62 15.58 1.50e+00 4.44e-01 1.08e+02 ... (remaining 116505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 27972 35.28 - 70.55: 1280 70.55 - 105.83: 22 105.83 - 141.11: 1 141.11 - 176.38: 4 Dihedral angle restraints: 29279 sinusoidal: 17303 harmonic: 11976 Sorted by residual: dihedral pdb=" CA ARG I 83 " pdb=" C ARG I 83 " pdb=" N PHE I 84 " pdb=" CA PHE I 84 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" C LEU B 60 " pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" CB LEU B 60 " ideal model delta harmonic sigma weight residual -122.60 -134.42 11.82 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" CA PRO D 641 " pdb=" C PRO D 641 " pdb=" N PRO D 642 " pdb=" CA PRO D 642 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 29276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4991 0.104 - 0.209: 163 0.209 - 0.313: 0 0.313 - 0.418: 3 0.418 - 0.522: 5 Chirality restraints: 5162 Sorted by residual: chirality pdb=" P DC Q 12 " pdb=" OP1 DC Q 12 " pdb=" OP2 DC Q 12 " pdb=" O5' DC Q 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P DC Q 21 " pdb=" OP1 DC Q 21 " pdb=" OP2 DC Q 21 " pdb=" O5' DC Q 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" P DG Q 22 " pdb=" OP1 DG Q 22 " pdb=" OP2 DG Q 22 " pdb=" O5' DG Q 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 5159 not shown) Planarity restraints: 9151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C1142 " 0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C SER C1142 " -0.084 2.00e-02 2.50e+03 pdb=" O SER C1142 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP C1143 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 255 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO I 256 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 28 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N1 DC O 28 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DC O 28 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC O 28 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC O 28 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC O 28 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC O 28 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC O 28 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC O 28 " 0.006 2.00e-02 2.50e+03 pdb=" H5 DC O 28 " -0.004 2.00e-02 2.50e+03 pdb=" H6 DC O 28 " 0.003 2.00e-02 2.50e+03 ... (remaining 9148 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1954 2.15 - 2.76: 117945 2.76 - 3.37: 173370 3.37 - 3.99: 224087 3.99 - 4.60: 351173 Nonbonded interactions: 868529 Sorted by model distance: nonbonded pdb=" H ASN C 510 " pdb=" O PHE C 514 " model vdw 1.537 2.450 nonbonded pdb=" OE1 GLU H 43 " pdb=" H GLU H 43 " model vdw 1.572 2.450 nonbonded pdb=" O PRO D 434 " pdb=" HZ3 LYS D 712 " model vdw 1.583 2.450 nonbonded pdb=" O THR C 491 " pdb="HD21 ASN C 613 " model vdw 1.584 2.450 nonbonded pdb=" OD1 ASP D 626 " pdb=" HE ARG D 660 " model vdw 1.586 2.450 ... (remaining 868524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.820 Extract box with map and model: 1.920 Check model and map are aligned: 0.370 Set scattering table: 0.460 Process input model: 159.540 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.140 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.003 0.058 33110 Z= 0.177 Angle : 0.521 15.818 45389 Z= 0.292 Chirality : 0.044 0.522 5162 Planarity : 0.003 0.049 5455 Dihedral : 17.511 176.384 12932 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3757 helix: 1.77 (0.14), residues: 1505 sheet: 0.05 (0.26), residues: 410 loop : -0.96 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 718 HIS 0.007 0.001 HIS D 505 PHE 0.019 0.001 PHE C 376 TYR 0.021 0.001 TYR E 32 ARG 0.005 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.8173 time to fit residues: 220.6366 Evaluate side-chains 143 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 349 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN I 224 ASN I 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33110 Z= 0.236 Angle : 0.524 5.195 45389 Z= 0.292 Chirality : 0.042 0.371 5162 Planarity : 0.004 0.057 5455 Dihedral : 17.669 176.130 5678 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3757 helix: 1.63 (0.14), residues: 1541 sheet: 0.02 (0.27), residues: 401 loop : -1.05 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1203 HIS 0.008 0.001 HIS D 505 PHE 0.014 0.001 PHE C 442 TYR 0.017 0.001 TYR E 32 ARG 0.005 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 149 average time/residue: 0.7722 time to fit residues: 192.9599 Evaluate side-chains 147 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 347 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 280 optimal weight: 0.0570 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33110 Z= 0.227 Angle : 0.505 6.043 45389 Z= 0.280 Chirality : 0.041 0.376 5162 Planarity : 0.004 0.059 5455 Dihedral : 17.625 176.755 5678 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3757 helix: 1.69 (0.14), residues: 1549 sheet: -0.14 (0.27), residues: 407 loop : -1.04 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.008 0.001 HIS D 505 PHE 0.016 0.001 PHE C 376 TYR 0.016 0.001 TYR E 32 ARG 0.004 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8283 (t) cc_final: 0.8027 (t) outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.8266 time to fit residues: 210.8282 Evaluate side-chains 149 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33110 Z= 0.349 Angle : 0.541 5.278 45389 Z= 0.300 Chirality : 0.043 0.376 5162 Planarity : 0.004 0.060 5455 Dihedral : 17.680 176.247 5678 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.48 % Allowed : 5.58 % Favored : 93.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3757 helix: 1.55 (0.13), residues: 1547 sheet: -0.19 (0.26), residues: 419 loop : -1.16 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 83 HIS 0.008 0.001 HIS D 505 PHE 0.016 0.002 PHE C 909 TYR 0.016 0.001 TYR E 32 ARG 0.004 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8316 (t) cc_final: 0.8085 (t) REVERT: A 95 MET cc_start: 0.9216 (ptt) cc_final: 0.8822 (ptt) REVERT: D 784 MET cc_start: 0.8633 (ttp) cc_final: 0.8419 (ttp) outliers start: 15 outliers final: 9 residues processed: 154 average time/residue: 0.7818 time to fit residues: 200.3351 Evaluate side-chains 152 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 334 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33110 Z= 0.256 Angle : 0.515 5.811 45389 Z= 0.286 Chirality : 0.041 0.389 5162 Planarity : 0.004 0.060 5455 Dihedral : 17.682 176.671 5678 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.41 % Allowed : 6.73 % Favored : 92.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3757 helix: 1.62 (0.14), residues: 1548 sheet: -0.19 (0.27), residues: 407 loop : -1.11 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1203 HIS 0.006 0.001 HIS D 505 PHE 0.013 0.001 PHE C 909 TYR 0.012 0.001 TYR E 32 ARG 0.002 0.000 ARG I 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8307 (t) cc_final: 0.8072 (t) outliers start: 13 outliers final: 12 residues processed: 152 average time/residue: 0.7961 time to fit residues: 200.8691 Evaluate side-chains 155 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 1.9990 chunk 335 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33110 Z= 0.257 Angle : 0.512 6.560 45389 Z= 0.284 Chirality : 0.041 0.385 5162 Planarity : 0.004 0.058 5455 Dihedral : 17.691 177.031 5678 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.41 % Allowed : 7.24 % Favored : 92.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3757 helix: 1.65 (0.14), residues: 1549 sheet: -0.21 (0.27), residues: 408 loop : -1.12 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 83 HIS 0.007 0.001 HIS D 505 PHE 0.013 0.001 PHE C 376 TYR 0.014 0.001 TYR E 32 ARG 0.003 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8312 (t) cc_final: 0.8090 (t) REVERT: A 95 MET cc_start: 0.9226 (ptt) cc_final: 0.8920 (ptt) outliers start: 13 outliers final: 12 residues processed: 154 average time/residue: 0.7919 time to fit residues: 203.0696 Evaluate side-chains 156 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33110 Z= 0.223 Angle : 0.502 6.479 45389 Z= 0.279 Chirality : 0.041 0.386 5162 Planarity : 0.004 0.057 5455 Dihedral : 17.689 177.423 5678 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 7.65 % Favored : 91.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3757 helix: 1.72 (0.14), residues: 1547 sheet: -0.19 (0.27), residues: 408 loop : -1.09 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 83 HIS 0.006 0.001 HIS D 505 PHE 0.013 0.001 PHE F 249 TYR 0.012 0.001 TYR E 32 ARG 0.004 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8291 (t) cc_final: 0.8064 (t) outliers start: 13 outliers final: 13 residues processed: 153 average time/residue: 0.7910 time to fit residues: 201.0180 Evaluate side-chains 159 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 0.0980 chunk 183 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33110 Z= 0.163 Angle : 0.481 7.885 45389 Z= 0.267 Chirality : 0.040 0.385 5162 Planarity : 0.003 0.052 5455 Dihedral : 17.655 178.367 5678 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.26 % Allowed : 8.04 % Favored : 91.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3757 helix: 1.91 (0.14), residues: 1541 sheet: -0.12 (0.27), residues: 407 loop : -0.98 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 83 HIS 0.004 0.001 HIS D 505 PHE 0.014 0.001 PHE D 248 TYR 0.010 0.001 TYR A 168 ARG 0.006 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8316 (t) cc_final: 0.8094 (t) outliers start: 8 outliers final: 7 residues processed: 153 average time/residue: 0.7991 time to fit residues: 203.1403 Evaluate side-chains 153 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 324 optimal weight: 7.9990 chunk 345 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33110 Z= 0.231 Angle : 0.497 7.746 45389 Z= 0.275 Chirality : 0.041 0.386 5162 Planarity : 0.004 0.054 5455 Dihedral : 17.660 178.154 5678 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.29 % Allowed : 8.16 % Favored : 91.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3757 helix: 1.86 (0.14), residues: 1539 sheet: -0.16 (0.27), residues: 407 loop : -1.00 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 83 HIS 0.006 0.001 HIS D 505 PHE 0.017 0.001 PHE C 257 TYR 0.014 0.001 TYR C 283 ARG 0.004 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8278 (t) cc_final: 0.8052 (t) outliers start: 9 outliers final: 8 residues processed: 150 average time/residue: 0.7964 time to fit residues: 198.4902 Evaluate side-chains 154 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 383 optimal weight: 10.0000 chunk 353 optimal weight: 0.0030 chunk 305 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33110 Z= 0.349 Angle : 0.539 8.278 45389 Z= 0.297 Chirality : 0.043 0.387 5162 Planarity : 0.004 0.055 5455 Dihedral : 17.701 177.572 5678 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.35 % Allowed : 8.29 % Favored : 91.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3757 helix: 1.68 (0.13), residues: 1545 sheet: -0.25 (0.26), residues: 422 loop : -1.14 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1203 HIS 0.008 0.001 HIS C 482 PHE 0.015 0.001 PHE C 909 TYR 0.016 0.001 TYR C 283 ARG 0.005 0.000 ARG I 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8332 (t) cc_final: 0.8121 (t) REVERT: D 806 MET cc_start: 0.7913 (mmt) cc_final: 0.7508 (mmt) outliers start: 11 outliers final: 11 residues processed: 151 average time/residue: 0.8092 time to fit residues: 203.6656 Evaluate side-chains 156 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 5.9990 chunk 325 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 281 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081121 restraints weight = 174723.308| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.52 r_work: 0.3104 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33110 Z= 0.255 Angle : 0.512 6.599 45389 Z= 0.284 Chirality : 0.041 0.387 5162 Planarity : 0.004 0.054 5455 Dihedral : 17.701 177.885 5678 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.51 % Allowed : 8.26 % Favored : 91.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3757 helix: 1.73 (0.14), residues: 1546 sheet: -0.20 (0.27), residues: 407 loop : -1.08 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 83 HIS 0.006 0.001 HIS D 505 PHE 0.015 0.001 PHE D 248 TYR 0.016 0.001 TYR C 283 ARG 0.003 0.000 ARG C 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9257.52 seconds wall clock time: 159 minutes 15.74 seconds (9555.74 seconds total)