Starting phenix.real_space_refine on Sun Nov 19 03:05:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac1_15330/11_2023/8ac1_15330.pdb" } resolution = 4.06 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= 0.001 sd= 0.017 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 2 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 15685 2.51 5 N 4452 2.21 5 O 4911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 820": "OE1" <-> "OE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1214": "OD1" <-> "OD2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 913": "OE1" <-> "OE2" Residue "D GLU 1254": "OE1" <-> "OE2" Residue "D GLU 1281": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1767 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1759 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10402 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10377 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "N" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "R" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14377 SG CYS D 70 116.551 122.400 57.270 1.00337.21 S ATOM 14391 SG CYS D 72 115.803 125.875 58.684 1.00341.59 S ATOM 14499 SG CYS D 85 119.257 124.455 58.901 1.00344.86 S ATOM 14523 SG CYS D 88 116.486 122.957 61.027 1.00335.75 S ATOM 20211 SG CYS D 814 126.871 62.404 78.926 1.00110.73 S ATOM 20776 SG CYS D 888 123.060 63.440 78.654 1.00109.50 S ATOM 20827 SG CYS D 895 125.495 63.763 75.864 1.00 97.92 S ATOM 20848 SG CYS D 898 124.228 60.335 76.989 1.00101.02 S Time building chain proxies: 13.58, per 1000 atoms: 0.54 Number of scatterers: 25188 At special positions: 0 Unit cell: (149.988, 140.506, 160.332, 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 2 29.99 S 105 16.00 P 32 15.00 Mg 1 11.99 O 4911 8.00 N 4452 7.00 C 15685 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=0, symmetry=0 Time building additional restraints: 9.86 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5798 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 43 sheets defined 37.4% alpha, 15.2% beta 15 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 9.63 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.702A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.560A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 232 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.510A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.764A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.211A pdb=" N THR B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 4.121A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.859A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.904A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.115A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.188A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.698A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.880A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.592A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.726A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 609 through 612 Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.011A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 4.053A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.611A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 674' Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.717A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.033A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.517A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.633A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.634A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.843A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.700A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.781A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 231 removed outlier: 3.549A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.507A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.535A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 389 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 417 removed outlier: 4.236A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.730A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 458 " --> pdb=" O CYS D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 458' Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.512A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.864A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.875A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.675A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.041A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.753A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.306A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.875A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 876 removed outlier: 4.525A pdb=" N GLU D 873 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU D 874 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 876 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 4.084A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.176A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.093A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1294 removed outlier: 3.944A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.659A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.784A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.553A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 17 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 4.570A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 3.711A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.506A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 31 removed outlier: 5.759A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.613A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.734A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.914A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.553A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.499A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.834A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.530A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.937A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 637 removed outlier: 3.743A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 718 removed outlier: 7.314A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 783 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.874A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.701A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.548A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 838 removed outlier: 5.948A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.715A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.246A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 8.002A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.568A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD5, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD6, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.534A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.642A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 564 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 842 through 843 removed outlier: 4.218A pdb=" N ARG D 842 " --> pdb=" O LEU D 864 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.453A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 991 through 997 removed outlier: 3.662A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1025 through 1028 Processing sheet with id=AE3, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.622A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AE5, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 3.576A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.022A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1278 through 1279 957 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 12.14 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8293 1.34 - 1.45: 3146 1.45 - 1.57: 13943 1.57 - 1.69: 61 1.69 - 1.81: 182 Bond restraints: 25625 Sorted by residual: bond pdb=" CB MET C 805 " pdb=" CG MET C 805 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" CB GLN D 504 " pdb=" CG GLN D 504 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" SD MET C1290 " pdb=" CE MET C1290 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.58e+00 bond pdb=" CB GLU C1274 " pdb=" CG GLU C1274 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 25620 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.21: 469 104.21 - 111.66: 12067 111.66 - 119.12: 9060 119.12 - 126.57: 12823 126.57 - 134.02: 321 Bond angle restraints: 34740 Sorted by residual: angle pdb=" N ILE D 499 " pdb=" CA ILE D 499 " pdb=" C ILE D 499 " ideal model delta sigma weight residual 112.80 106.77 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" CA ARG D 77 " pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.64e+00 angle pdb=" N GLY D 496 " pdb=" CA GLY D 496 " pdb=" C GLY D 496 " ideal model delta sigma weight residual 113.18 120.25 -7.07 2.37e+00 1.78e-01 8.89e+00 angle pdb=" N GLU C1024 " pdb=" CA GLU C1024 " pdb=" CB GLU C1024 " ideal model delta sigma weight residual 110.28 114.77 -4.49 1.55e+00 4.16e-01 8.38e+00 ... (remaining 34735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13954 17.87 - 35.73: 1385 35.73 - 53.60: 246 53.60 - 71.46: 64 71.46 - 89.33: 21 Dihedral angle restraints: 15670 sinusoidal: 6656 harmonic: 9014 Sorted by residual: dihedral pdb=" CA LYS D 76 " pdb=" C LYS D 76 " pdb=" N ARG D 77 " pdb=" CA ARG D 77 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN D 341 " pdb=" C ASN D 341 " pdb=" N LEU D 342 " pdb=" CA LEU D 342 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ILE D 820 " pdb=" C ILE D 820 " pdb=" N MET D 821 " pdb=" CA MET D 821 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 15667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2802 0.042 - 0.083: 869 0.083 - 0.125: 267 0.125 - 0.167: 34 0.167 - 0.209: 3 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA ARG D 77 " pdb=" N ARG D 77 " pdb=" C ARG D 77 " pdb=" CB ARG D 77 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE D1090 " pdb=" N ILE D1090 " pdb=" C ILE D1090 " pdb=" CB ILE D1090 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 3972 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.039 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP C1276 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " 0.020 2.00e-02 2.50e+03 1.47e-02 4.31e+00 pdb=" CG TYR C1229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 338 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PHE D 338 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE D 338 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG D 339 " -0.011 2.00e-02 2.50e+03 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 305 2.52 - 3.12: 20779 3.12 - 3.71: 42539 3.71 - 4.31: 55060 4.31 - 4.90: 88490 Nonbonded interactions: 207173 Sorted by model distance: nonbonded pdb=" N ASP D 464 " pdb="MG MG D1501 " model vdw 1.927 2.250 nonbonded pdb=" N GLY D 463 " pdb="MG MG D1501 " model vdw 2.091 2.250 nonbonded pdb=" O GLU D 652 " pdb=" OG SER D 655 " model vdw 2.135 2.440 nonbonded pdb=" NH1 ARG D1290 " pdb=" O LYS D1297 " model vdw 2.145 2.520 nonbonded pdb=" O GLU D1158 " pdb=" NH2 ARG D1206 " model vdw 2.147 2.520 ... (remaining 207168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 158 or resid 160 through 234)) selection = chain 'B' } 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: 3.300 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: 11.110 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 81.840 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.005 0.049 25625 Z= 0.303 Angle : 0.649 8.465 34740 Z= 0.342 Chirality : 0.044 0.209 3975 Planarity : 0.004 0.039 4443 Dihedral : 14.808 89.329 9872 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.14 (0.15), residues: 3121 helix: 0.26 (0.16), residues: 1055 sheet: -0.28 (0.27), residues: 391 loop : -1.58 (0.15), residues: 1675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.983 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3619 time to fit residues: 77.5616 Evaluate side-chains 103 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 282 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN C 406 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25625 Z= 0.201 Angle : 0.568 7.398 34740 Z= 0.296 Chirality : 0.042 0.167 3975 Planarity : 0.004 0.047 4443 Dihedral : 8.571 75.036 3766 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.15 % Allowed : 7.70 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3121 helix: 0.57 (0.16), residues: 1097 sheet: -0.26 (0.26), residues: 389 loop : -1.58 (0.15), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.3572 time to fit residues: 82.0771 Evaluate side-chains 107 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2683 time to fit residues: 4.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 282 optimal weight: 30.0000 chunk 305 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 226 optimal weight: 0.2980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN C 406 ASN C1209 GLN D 232 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25625 Z= 0.153 Angle : 0.552 7.703 34740 Z= 0.282 Chirality : 0.042 0.171 3975 Planarity : 0.003 0.050 4443 Dihedral : 8.419 75.289 3766 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.84 (0.15), residues: 3121 helix: 0.68 (0.16), residues: 1100 sheet: -0.15 (0.27), residues: 373 loop : -1.57 (0.15), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 146 average time/residue: 0.3772 time to fit residues: 93.6376 Evaluate side-chains 114 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 135 optimal weight: 8.9990 chunk 189 optimal weight: 0.1980 chunk 283 optimal weight: 50.0000 chunk 300 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 overall best weight: 1.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1209 GLN D 340 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 700 ASN D 921 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25625 Z= 0.152 Angle : 0.541 8.259 34740 Z= 0.275 Chirality : 0.042 0.166 3975 Planarity : 0.003 0.050 4443 Dihedral : 8.345 75.233 3766 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.15), residues: 3121 helix: 0.79 (0.16), residues: 1097 sheet: -0.26 (0.26), residues: 379 loop : -1.58 (0.15), residues: 1645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3825 time to fit residues: 92.6105 Evaluate side-chains 115 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 406 ASN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 300 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25625 Z= 0.408 Angle : 0.700 7.826 34740 Z= 0.365 Chirality : 0.045 0.179 3975 Planarity : 0.005 0.047 4443 Dihedral : 8.924 84.550 3766 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.15), residues: 3121 helix: 0.51 (0.16), residues: 1076 sheet: -0.59 (0.26), residues: 387 loop : -1.74 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3940 time to fit residues: 83.2539 Evaluate side-chains 104 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN C 406 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25625 Z= 0.289 Angle : 0.622 7.492 34740 Z= 0.321 Chirality : 0.044 0.190 3975 Planarity : 0.004 0.050 4443 Dihedral : 8.890 86.910 3766 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.12 (0.15), residues: 3121 helix: 0.60 (0.16), residues: 1076 sheet: -0.63 (0.26), residues: 387 loop : -1.74 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.3869 time to fit residues: 83.7659 Evaluate side-chains 106 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN C 406 ASN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25625 Z= 0.371 Angle : 0.680 9.382 34740 Z= 0.353 Chirality : 0.045 0.201 3975 Planarity : 0.005 0.087 4443 Dihedral : 9.056 89.788 3766 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.15), residues: 3121 helix: 0.41 (0.16), residues: 1084 sheet: -0.68 (0.26), residues: 378 loop : -1.91 (0.14), residues: 1659 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3865 time to fit residues: 81.4534 Evaluate side-chains 107 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 190 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 272 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25625 Z= 0.267 Angle : 0.628 7.603 34740 Z= 0.324 Chirality : 0.044 0.215 3975 Planarity : 0.004 0.051 4443 Dihedral : 8.961 88.900 3766 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.23 (0.15), residues: 3121 helix: 0.54 (0.16), residues: 1077 sheet: -0.76 (0.26), residues: 378 loop : -1.81 (0.15), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3728 time to fit residues: 83.2094 Evaluate side-chains 108 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 40.0000 chunk 262 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 0.0010 chunk 252 optimal weight: 10.0000 chunk 264 optimal weight: 0.0970 chunk 278 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 overall best weight: 3.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25625 Z= 0.257 Angle : 0.628 7.781 34740 Z= 0.322 Chirality : 0.044 0.227 3975 Planarity : 0.004 0.051 4443 Dihedral : 8.892 88.168 3766 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.18 (0.15), residues: 3121 helix: 0.58 (0.16), residues: 1078 sheet: -0.64 (0.26), residues: 370 loop : -1.80 (0.15), residues: 1673 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3789 time to fit residues: 83.5158 Evaluate side-chains 108 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 151 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25625 Z= 0.243 Angle : 0.623 7.599 34740 Z= 0.319 Chirality : 0.044 0.216 3975 Planarity : 0.004 0.054 4443 Dihedral : 8.846 87.445 3766 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.15), residues: 3121 helix: 0.61 (0.16), residues: 1079 sheet: -0.75 (0.25), residues: 380 loop : -1.78 (0.15), residues: 1662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3726 time to fit residues: 82.2142 Evaluate side-chains 111 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.061080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045925 restraints weight = 180096.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047265 restraints weight = 116176.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.047681 restraints weight = 73971.959| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25625 Z= 0.215 Angle : 0.616 7.987 34740 Z= 0.314 Chirality : 0.043 0.215 3975 Planarity : 0.004 0.055 4443 Dihedral : 8.768 87.156 3766 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.14 (0.15), residues: 3121 helix: 0.63 (0.16), residues: 1086 sheet: -0.76 (0.26), residues: 380 loop : -1.77 (0.15), residues: 1655 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3889.92 seconds wall clock time: 73 minutes 14.93 seconds (4394.93 seconds total)