Starting phenix.real_space_refine on Wed Jun 18 14:28:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.map" model { file = "/net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zoq_14848/06_2025/7zoq_14848.cif" } resolution = 3.2 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= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 38 5.49 5 S 73 5.16 5 C 13121 2.51 5 N 3653 2.21 5 O 3977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20866 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6637 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 28, 'TRANS': 783} Chain breaks: 1 Chain: "B" Number of atoms: 13412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 Conformer: "B" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 bond proxies already assigned to first conformer: 13670 Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 813 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 3, 'rna3p_pyr': 12} Link IDs: {'rna2p': 22, 'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14061 SG CYS B 997 45.028 71.327 125.559 1.00 24.19 S ATOM 17761 SG CYS B1515 43.831 70.092 122.214 1.00 23.98 S ATOM 18010 SG CYS B1545 42.632 73.448 123.760 1.00 20.16 S ATOM 18028 SG CYS B1548 46.094 73.164 122.336 1.00 18.28 S ATOM 7316 SG CYS B 97 92.075 75.162 39.769 1.00 41.05 S ATOM 7591 SG CYS B 131 95.146 73.201 38.468 1.00 63.59 S ATOM 7641 SG CYS B 137 95.354 75.246 41.719 1.00 42.75 S ATOM 7665 SG CYS B 140 93.216 72.148 41.559 1.00 37.66 S ATOM 10363 SG CYS B 498 65.453 80.350 63.928 1.00 34.05 S ATOM 10440 SG CYS B 508 66.298 79.054 60.534 1.00 41.08 S ATOM 10452 SG CYS B 510 66.669 82.823 61.196 1.00 30.22 S ATOM 10472 SG CYS B 513 69.050 80.320 62.816 1.00 28.09 S ATOM 12156 SG CYS B 757 43.748 79.067 87.105 1.00 51.71 S ATOM 12168 SG CYS B 759 45.021 82.313 88.698 1.00 36.29 S ATOM 12189 SG CYS B 762 47.548 79.648 87.573 1.00 31.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B1526 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B1526 " occ=0.50 Time building chain proxies: 18.10, per 1000 atoms: 0.87 Number of scatterers: 20866 At special positions: 0 Unit cell: (122.582, 123.859, 219.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 73 16.00 P 38 15.00 O 3977 8.00 N 3653 7.00 C 13121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 997 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1545 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1548 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1515 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 140 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 97 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 137 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 131 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 508 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 513 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 510 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" ND1 HIS B 754 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 759 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 757 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 762 " Number of angles added : 21 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 40.9% alpha, 10.5% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 60 through 79 Processing helix chain 'A' and resid 83 through 118 removed outlier: 4.001A pdb=" N ASN A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 149 removed outlier: 4.104A pdb=" N LYS A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.731A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.772A pdb=" N LYS A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 removed outlier: 4.482A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 5.783A pdb=" N PHE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.817A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 removed outlier: 4.197A pdb=" N GLU A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 4.571A pdb=" N VAL A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 Processing helix chain 'A' and resid 400 through 418 removed outlier: 4.248A pdb=" N ALA A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.581A pdb=" N GLU A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 533 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.940A pdb=" N LYS A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU A 539 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 540 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 557 through 560 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.902A pdb=" N ASN A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.849A pdb=" N HIS A 591 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.873A pdb=" N LYS A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 removed outlier: 4.189A pdb=" N SER A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.511A pdb=" N ILE A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 removed outlier: 3.516A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 Processing helix chain 'A' and resid 707 through 713 removed outlier: 4.218A pdb=" N LEU A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 766 through 780 removed outlier: 3.695A pdb=" N VAL A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 removed outlier: 3.549A pdb=" N LYS A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 800 through 808 removed outlier: 3.675A pdb=" N LEU A 804 " --> pdb=" O GLN A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.569A pdb=" N ARG B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 68 through 87 removed outlier: 4.081A pdb=" N VAL B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 145 through 148 removed outlier: 3.524A pdb=" N LYS B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 148' Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 291 through 310 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 329 removed outlier: 4.004A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.874A pdb=" N PHE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 401 Processing helix chain 'B' and resid 478 through 495 removed outlier: 3.534A pdb=" N LEU B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.947A pdb=" N CYS B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.553A pdb=" N GLN B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.682A pdb=" N THR B 602 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 630 removed outlier: 3.924A pdb=" N THR B 629 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.595A pdb=" N LEU B 675 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 748 removed outlier: 3.522A pdb=" N PHE B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 858 through 862 removed outlier: 3.794A pdb=" N GLY B 862 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.686A pdb=" N LYS B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 995 removed outlier: 4.162A pdb=" N ILE B 982 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1065 removed outlier: 3.525A pdb=" N ASN B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 4.194A pdb=" N LEU B1079 " --> pdb=" O THR B1075 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1084 " --> pdb=" O GLU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1101 Proline residue: B1097 - end of helix Processing helix chain 'B' and resid 1107 through 1120 removed outlier: 3.725A pdb=" N ASP B1114 " --> pdb=" O THR B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1124 Processing helix chain 'B' and resid 1125 through 1133 Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.807A pdb=" N LEU B1145 " --> pdb=" O THR B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1165 removed outlier: 4.025A pdb=" N LEU B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1184 removed outlier: 3.560A pdb=" N VAL B1184 " --> pdb=" O LEU B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1196 removed outlier: 3.545A pdb=" N LEU B1196 " --> pdb=" O ILE B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1199 No H-bonds generated for 'chain 'B' and resid 1197 through 1199' Processing helix chain 'B' and resid 1206 through 1216 Processing helix chain 'B' and resid 1219 through 1229 removed outlier: 3.930A pdb=" N VAL B1223 " --> pdb=" O PRO B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1259 removed outlier: 3.885A pdb=" N HIS B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1274 through 1283 Processing helix chain 'B' and resid 1431 through 1452 removed outlier: 3.925A pdb=" N GLU B1435 " --> pdb=" O PRO B1431 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B1445 " --> pdb=" O THR B1441 " (cutoff:3.500A) Processing helix chain 'B' and resid 1500 through 1504 removed outlier: 3.548A pdb=" N ARG B1503 " --> pdb=" O VAL B1500 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1523 removed outlier: 3.920A pdb=" N ASP B1521 " --> pdb=" O GLU B1518 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B1522 " --> pdb=" O ILE B1519 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B1523 " --> pdb=" O LEU B1520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1518 through 1523' Processing helix chain 'B' and resid 1524 through 1532 Processing helix chain 'B' and resid 1545 through 1552 Processing helix chain 'B' and resid 1574 through 1579 removed outlier: 3.890A pdb=" N ASN B1577 " --> pdb=" O LEU B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1613 through 1621 removed outlier: 3.568A pdb=" N VAL B1617 " --> pdb=" O GLY B1613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1671 Processing helix chain 'B' and resid 1683 through 1687 Processing helix chain 'B' and resid 1706 through 1723 removed outlier: 3.572A pdb=" N LEU B1710 " --> pdb=" O ASP B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1736 removed outlier: 3.502A pdb=" N LEU B1736 " --> pdb=" O LEU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1763 through 1768 Processing helix chain 'B' and resid 1772 through 1777 removed outlier: 3.840A pdb=" N GLN B1776 " --> pdb=" O TYR B1772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.741A pdb=" N ASN A 496 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 489 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 482 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE A 585 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 484 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 663 through 664 removed outlier: 3.536A pdb=" N GLU A 639 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR A 761 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 758 " --> pdb=" O TYR A 813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.464A pdb=" N HIS A 687 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.561A pdb=" N TYR B 254 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.512A pdb=" N ARG B 185 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.528A pdb=" N ARG B 53 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 66 " --> pdb=" O ARG B 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.851A pdb=" N TYR B 91 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 188 through 190 removed outlier: 6.767A pdb=" N ARG B 189 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 519 through 521 removed outlier: 3.530A pdb=" N GLY B 441 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 613 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 442 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN B 611 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 444 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 609 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.953A pdb=" N LYS B 466 " --> pdb=" O TRP B 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 476 through 477 removed outlier: 3.648A pdb=" N SER B 524 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 534 through 538 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.783A pdb=" N THR B 547 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 653 through 662 removed outlier: 4.759A pdb=" N LYS B 822 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR B 728 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 727 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 653 through 662 Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'B' and resid 902 through 904 removed outlier: 4.208A pdb=" N GLY B1789 " --> pdb=" O ILE B 903 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 907 through 910 Processing sheet with id=AC2, first strand: chain 'B' and resid 1560 through 1562 removed outlier: 3.518A pdb=" N PHE B1651 " --> pdb=" O CYS B 943 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR B 937 " --> pdb=" O ASN B1657 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 940 " --> pdb=" O ILE B1698 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE B1698 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 942 " --> pdb=" O GLY B1696 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.826A pdb=" N GLU B 957 " --> pdb=" O ASP B 967 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP B 967 " --> pdb=" O GLU B 957 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 965 " --> pdb=" O GLN B 959 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1044 through 1047 Processing sheet with id=AC5, first strand: chain 'B' and resid 1169 through 1170 removed outlier: 3.517A pdb=" N VAL B1138 " --> pdb=" O TYR B1170 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG B1135 " --> pdb=" O ARG B1204 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B1204 " --> pdb=" O ARG B1135 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS B1137 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B1139 " --> pdb=" O ASP B1200 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B1200 " --> pdb=" O ARG B1139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1378 through 1379 removed outlier: 3.780A pdb=" N ARG B1391 " --> pdb=" O ILE B1379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1474 through 1477 removed outlier: 4.039A pdb=" N ARG B1476 " --> pdb=" O ASP B1486 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP B1486 " --> pdb=" O ARG B1476 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1581 through 1583 removed outlier: 4.349A pdb=" N ARG B1638 " --> pdb=" O LEU B1583 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3731 1.32 - 1.45: 5496 1.45 - 1.57: 11966 1.57 - 1.70: 76 1.70 - 1.82: 108 Bond restraints: 21377 Sorted by residual: bond pdb=" C BLYS B1526 " pdb=" N GLU B1527 " ideal model delta sigma weight residual 1.334 1.418 -0.084 1.33e-02 5.65e+03 4.00e+01 bond pdb=" C GLN B1525 " pdb=" N BLYS B1526 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.31e-02 5.83e+03 2.52e+01 bond pdb=" N ARG B 409 " pdb=" CA ARG B 409 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" C ALA B 305 " pdb=" O ALA B 305 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.17e-02 7.31e+03 1.04e+01 ... (remaining 21372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 28802 3.20 - 6.39: 169 6.39 - 9.59: 22 9.59 - 12.79: 1 12.79 - 15.98: 1 Bond angle restraints: 28995 Sorted by residual: angle pdb=" N PRO B 277 " pdb=" CA PRO B 277 " pdb=" CB PRO B 277 " ideal model delta sigma weight residual 101.83 110.02 -8.19 8.40e-01 1.42e+00 9.51e+01 angle pdb=" N PRO B 289 " pdb=" CA PRO B 289 " pdb=" CB PRO B 289 " ideal model delta sigma weight residual 103.08 111.55 -8.47 9.70e-01 1.06e+00 7.62e+01 angle pdb=" C TYR A 766 " pdb=" CA TYR A 766 " pdb=" CB TYR A 766 " ideal model delta sigma weight residual 109.51 125.49 -15.98 1.85e+00 2.92e-01 7.46e+01 angle pdb=" N PRO B1356 " pdb=" CA PRO B1356 " pdb=" CB PRO B1356 " ideal model delta sigma weight residual 103.25 112.24 -8.99 1.05e+00 9.07e-01 7.33e+01 angle pdb=" N PRO B1049 " pdb=" CA PRO B1049 " pdb=" CB PRO B1049 " ideal model delta sigma weight residual 103.25 111.50 -8.25 1.05e+00 9.07e-01 6.17e+01 ... (remaining 28990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 12627 33.45 - 66.90: 420 66.90 - 100.35: 36 100.35 - 133.80: 3 133.80 - 167.25: 6 Dihedral angle restraints: 13092 sinusoidal: 5755 harmonic: 7337 Sorted by residual: dihedral pdb=" O4' U C 16 " pdb=" C1' U C 16 " pdb=" N1 U C 16 " pdb=" C2 U C 16 " ideal model delta sinusoidal sigma weight residual -160.00 7.25 -167.25 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 200.00 43.69 156.31 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual 200.00 53.92 146.08 1 1.50e+01 4.44e-03 7.81e+01 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2994 0.102 - 0.203: 155 0.203 - 0.305: 12 0.305 - 0.407: 1 0.407 - 0.508: 1 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CA TYR A 766 " pdb=" N TYR A 766 " pdb=" C TYR A 766 " pdb=" CB TYR A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" C1' U C 27 " pdb=" O4' U C 27 " pdb=" C2' U C 27 " pdb=" N1 U C 27 " both_signs ideal model delta sigma weight residual False 2.45 2.08 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO B1345 " pdb=" N PRO B1345 " pdb=" C PRO B1345 " pdb=" CB PRO B1345 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3160 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1096 " 0.081 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO B1097 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO B1097 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO B1097 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B1430 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO B1431 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B1431 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1431 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1521 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ASP B1521 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP B1521 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B1522 " 0.022 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3052 2.76 - 3.29: 19266 3.29 - 3.83: 32250 3.83 - 4.36: 37394 4.36 - 4.90: 65422 Nonbonded interactions: 157384 Sorted by model distance: nonbonded pdb=" NZ LYS A 310 " pdb=" OG1 THR A 313 " model vdw 2.223 3.120 nonbonded pdb=" O ARG A 208 " pdb=" OG1 THR A 212 " model vdw 2.228 3.040 nonbonded pdb=" O LYS B1446 " pdb=" NE2 GLN B1450 " model vdw 2.230 3.120 nonbonded pdb=" O PRO B 923 " pdb=" OH TYR B1556 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 573 " pdb=" OD1 ASP B 575 " model vdw 2.239 3.040 ... (remaining 157379 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 64.980 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 0.084 21393 Z= 0.195 Angle : 0.655 15.983 29016 Z= 0.405 Chirality : 0.047 0.508 3163 Planarity : 0.005 0.119 3599 Dihedral : 16.618 167.248 8336 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.54 % Favored : 91.70 % Rotamer: Outliers : 0.81 % Allowed : 0.43 % Favored : 98.77 % Cbeta Deviations : 0.04 % 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: 0.03 (0.18), residues: 2497 helix: 2.07 (0.18), residues: 898 sheet: 0.07 (0.32), residues: 302 loop : -1.58 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1788 HIS 0.007 0.001 HIS A 657 PHE 0.017 0.001 PHE B 201 TYR 0.019 0.001 TYR B1444 ARG 0.006 0.000 ARG B 786 Details of bonding type rmsd hydrogen bonds : bond 0.16015 ( 751) hydrogen bonds : angle 5.70734 ( 2157) metal coordination : bond 0.00565 ( 16) metal coordination : angle 2.32482 ( 21) covalent geometry : bond 0.00316 (21377) covalent geometry : angle 0.65248 (28995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.7060 (t80) REVERT: B 555 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6978 (p0) REVERT: B 1128 MET cc_start: 0.3967 (ttm) cc_final: 0.3517 (mmm) outliers start: 15 outliers final: 6 residues processed: 193 average time/residue: 0.3652 time to fit residues: 107.7947 Evaluate side-chains 147 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1528 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 0.0370 chunk 65 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS B1447 ASN B1450 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 ASN ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.144660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105270 restraints weight = 64218.050| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.72 r_work: 0.3343 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21393 Z= 0.129 Angle : 0.570 11.986 29016 Z= 0.292 Chirality : 0.041 0.242 3163 Planarity : 0.004 0.083 3599 Dihedral : 13.270 161.676 3344 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.70 % Favored : 91.82 % Rotamer: Outliers : 0.85 % Allowed : 5.56 % Favored : 93.59 % 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: 0.02 (0.17), residues: 2497 helix: 2.11 (0.18), residues: 902 sheet: 0.08 (0.32), residues: 299 loop : -1.63 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1788 HIS 0.004 0.001 HIS A 146 PHE 0.021 0.001 PHE B1457 TYR 0.018 0.001 TYR A 766 ARG 0.007 0.000 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 751) hydrogen bonds : angle 4.46610 ( 2157) metal coordination : bond 0.00971 ( 16) metal coordination : angle 2.21961 ( 21) covalent geometry : bond 0.00288 (21377) covalent geometry : angle 0.56716 (28995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 2.136 Fit side-chains REVERT: A 492 LYS cc_start: 0.7771 (tppt) cc_final: 0.7470 (tptt) REVERT: B 394 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 1430 GLN cc_start: 0.7789 (tp40) cc_final: 0.7447 (mm110) outliers start: 16 outliers final: 7 residues processed: 157 average time/residue: 0.3447 time to fit residues: 85.1024 Evaluate side-chains 141 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 946 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 219 optimal weight: 0.0170 chunk 227 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 1 optimal weight: 0.0370 chunk 152 optimal weight: 0.8980 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105455 restraints weight = 64875.484| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.77 r_work: 0.3345 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21393 Z= 0.109 Angle : 0.540 10.392 29016 Z= 0.274 Chirality : 0.040 0.227 3163 Planarity : 0.004 0.074 3599 Dihedral : 13.094 162.447 3326 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.18 % Favored : 92.34 % Rotamer: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.17), residues: 2497 helix: 2.13 (0.18), residues: 901 sheet: 0.24 (0.32), residues: 292 loop : -1.63 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1788 HIS 0.008 0.001 HIS B1371 PHE 0.018 0.001 PHE B 201 TYR 0.012 0.001 TYR A 685 ARG 0.005 0.000 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 751) hydrogen bonds : angle 4.18835 ( 2157) metal coordination : bond 0.00829 ( 16) metal coordination : angle 2.14344 ( 21) covalent geometry : bond 0.00242 (21377) covalent geometry : angle 0.53671 (28995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 2.397 Fit side-chains REVERT: A 164 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 492 LYS cc_start: 0.7809 (tppt) cc_final: 0.7411 (tptt) REVERT: B 394 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7692 (t80) REVERT: B 524 SER cc_start: 0.9119 (p) cc_final: 0.8840 (t) REVERT: B 531 GLU cc_start: 0.8683 (mp0) cc_final: 0.7943 (mp0) REVERT: B 647 ASP cc_start: 0.7196 (m-30) cc_final: 0.6907 (m-30) REVERT: B 1430 GLN cc_start: 0.7810 (tp40) cc_final: 0.7497 (mm110) outliers start: 13 outliers final: 7 residues processed: 157 average time/residue: 0.3583 time to fit residues: 88.4521 Evaluate side-chains 143 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN B 400 GLN B 446 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 ASN ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098888 restraints weight = 83261.682| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 5.01 r_work: 0.3197 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21393 Z= 0.242 Angle : 0.687 11.470 29016 Z= 0.352 Chirality : 0.046 0.397 3163 Planarity : 0.005 0.068 3599 Dihedral : 13.540 177.264 3324 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.94 % Favored : 90.46 % Rotamer: Outliers : 1.33 % Allowed : 8.78 % Favored : 89.89 % 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: -0.48 (0.17), residues: 2497 helix: 1.71 (0.18), residues: 903 sheet: -0.47 (0.31), residues: 310 loop : -1.87 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1788 HIS 0.007 0.002 HIS B1610 PHE 0.025 0.002 PHE B 201 TYR 0.018 0.002 TYR A 685 ARG 0.008 0.001 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.05533 ( 751) hydrogen bonds : angle 4.53198 ( 2157) metal coordination : bond 0.01626 ( 16) metal coordination : angle 2.58647 ( 21) covalent geometry : bond 0.00567 (21377) covalent geometry : angle 0.68386 (28995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 492 LYS cc_start: 0.8023 (tppt) cc_final: 0.7665 (tptt) REVERT: A 662 LYS cc_start: 0.8362 (mppt) cc_final: 0.7764 (mptt) REVERT: B 394 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 510 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7084 (p) REVERT: B 770 ASN cc_start: 0.8926 (m-40) cc_final: 0.8694 (m-40) REVERT: B 895 MET cc_start: 0.6546 (tpt) cc_final: 0.6254 (tpt) REVERT: B 1471 ASP cc_start: 0.7092 (m-30) cc_final: 0.6685 (m-30) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.3800 time to fit residues: 89.9987 Evaluate side-chains 150 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1442 GLN Chi-restraints excluded: chain B residue 1483 THR Chi-restraints excluded: chain B residue 1524 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1739 ASN ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102235 restraints weight = 72063.423| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.67 r_work: 0.3262 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21393 Z= 0.121 Angle : 0.569 10.941 29016 Z= 0.289 Chirality : 0.041 0.262 3163 Planarity : 0.004 0.066 3599 Dihedral : 13.313 177.993 3324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.06 % Favored : 92.38 % Rotamer: Outliers : 1.14 % Allowed : 9.78 % Favored : 89.08 % 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: -0.28 (0.17), residues: 2497 helix: 1.90 (0.18), residues: 902 sheet: -0.18 (0.32), residues: 309 loop : -1.83 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1788 HIS 0.003 0.001 HIS B1610 PHE 0.021 0.001 PHE B 201 TYR 0.015 0.001 TYR A 685 ARG 0.005 0.000 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 751) hydrogen bonds : angle 4.20892 ( 2157) metal coordination : bond 0.01094 ( 16) metal coordination : angle 2.36776 ( 21) covalent geometry : bond 0.00275 (21377) covalent geometry : angle 0.56571 (28995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 492 LYS cc_start: 0.7901 (tppt) cc_final: 0.7529 (tptt) REVERT: A 788 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6960 (mptt) REVERT: B 325 LEU cc_start: 0.8354 (mm) cc_final: 0.7992 (mm) REVERT: B 394 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 510 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6711 (p) REVERT: B 531 GLU cc_start: 0.8657 (mp0) cc_final: 0.7925 (mp0) REVERT: B 770 ASN cc_start: 0.8792 (m-40) cc_final: 0.8526 (m-40) REVERT: B 895 MET cc_start: 0.6510 (tpt) cc_final: 0.6208 (tpt) REVERT: B 1438 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7030 (mmtm) REVERT: B 1457 PHE cc_start: 0.6433 (t80) cc_final: 0.6087 (t80) REVERT: B 1471 ASP cc_start: 0.7119 (m-30) cc_final: 0.6773 (m-30) REVERT: B 1525 GLN cc_start: 0.6539 (tp40) cc_final: 0.6320 (tp40) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.3711 time to fit residues: 89.7391 Evaluate side-chains 152 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1442 GLN Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1634 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 232 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 119 optimal weight: 0.0000 chunk 93 optimal weight: 3.9990 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100176 restraints weight = 62436.150| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.07 r_work: 0.3234 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21393 Z= 0.209 Angle : 0.641 10.695 29016 Z= 0.327 Chirality : 0.044 0.317 3163 Planarity : 0.005 0.065 3599 Dihedral : 13.394 177.956 3324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.86 % Favored : 90.62 % Rotamer: Outliers : 1.33 % Allowed : 10.11 % Favored : 88.56 % 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: -0.51 (0.17), residues: 2497 helix: 1.72 (0.18), residues: 902 sheet: -0.38 (0.31), residues: 311 loop : -1.95 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 375 HIS 0.005 0.001 HIS B1610 PHE 0.026 0.002 PHE B 201 TYR 0.020 0.002 TYR B 49 ARG 0.006 0.001 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 751) hydrogen bonds : angle 4.40020 ( 2157) metal coordination : bond 0.01307 ( 16) metal coordination : angle 2.45829 ( 21) covalent geometry : bond 0.00491 (21377) covalent geometry : angle 0.63765 (28995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 492 LYS cc_start: 0.8082 (tppt) cc_final: 0.7505 (tptp) REVERT: A 662 LYS cc_start: 0.8302 (mppt) cc_final: 0.7600 (mptt) REVERT: A 788 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6914 (mptt) REVERT: B 394 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 440 LYS cc_start: 0.8718 (tptt) cc_final: 0.8395 (tptp) REVERT: B 510 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6872 (p) REVERT: B 531 GLU cc_start: 0.8618 (mp0) cc_final: 0.7781 (mp0) REVERT: B 647 ASP cc_start: 0.7521 (m-30) cc_final: 0.7054 (m-30) REVERT: B 770 ASN cc_start: 0.8890 (m-40) cc_final: 0.8619 (m-40) REVERT: B 895 MET cc_start: 0.6614 (tpt) cc_final: 0.6342 (tpt) REVERT: B 1438 LYS cc_start: 0.7410 (mmtt) cc_final: 0.6979 (mmtm) REVERT: B 1457 PHE cc_start: 0.6116 (t80) cc_final: 0.5704 (t80) REVERT: B 1471 ASP cc_start: 0.7212 (m-30) cc_final: 0.6834 (m-30) REVERT: B 1525 GLN cc_start: 0.7086 (tp40) cc_final: 0.6839 (tp40) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 0.3779 time to fit residues: 90.5428 Evaluate side-chains 153 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1634 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 41 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1525 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101960 restraints weight = 80255.703| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.56 r_work: 0.3256 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21393 Z= 0.127 Angle : 0.574 10.695 29016 Z= 0.291 Chirality : 0.041 0.304 3163 Planarity : 0.004 0.073 3599 Dihedral : 13.226 176.818 3324 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.06 % Favored : 92.46 % Rotamer: Outliers : 1.14 % Allowed : 11.21 % Favored : 87.65 % 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: -0.34 (0.17), residues: 2497 helix: 1.87 (0.18), residues: 902 sheet: -0.27 (0.32), residues: 309 loop : -1.87 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1788 HIS 0.003 0.001 HIS B1272 PHE 0.020 0.001 PHE B 201 TYR 0.016 0.001 TYR A 222 ARG 0.004 0.000 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 751) hydrogen bonds : angle 4.18452 ( 2157) metal coordination : bond 0.00980 ( 16) metal coordination : angle 2.32009 ( 21) covalent geometry : bond 0.00287 (21377) covalent geometry : angle 0.57049 (28995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 492 LYS cc_start: 0.7856 (tppt) cc_final: 0.7467 (tptt) REVERT: A 661 LYS cc_start: 0.7123 (pttp) cc_final: 0.6498 (tttm) REVERT: B 394 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 440 LYS cc_start: 0.8661 (tptt) cc_final: 0.8204 (mmtt) REVERT: B 510 CYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6730 (p) REVERT: B 531 GLU cc_start: 0.8686 (mp0) cc_final: 0.7938 (mp0) REVERT: B 647 ASP cc_start: 0.7387 (m-30) cc_final: 0.6925 (m-30) REVERT: B 770 ASN cc_start: 0.8789 (m-40) cc_final: 0.8505 (m-40) REVERT: B 895 MET cc_start: 0.6685 (tpt) cc_final: 0.6441 (tpt) REVERT: B 1437 PHE cc_start: 0.8224 (t80) cc_final: 0.7921 (t80) REVERT: B 1438 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6972 (mmtm) REVERT: B 1457 PHE cc_start: 0.6229 (t80) cc_final: 0.5844 (t80) REVERT: B 1471 ASP cc_start: 0.7173 (m-30) cc_final: 0.6824 (m-30) REVERT: B 1525 GLN cc_start: 0.7055 (tp-100) cc_final: 0.6782 (tp40) REVERT: B 1587 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: B 1627 ASP cc_start: 0.8358 (m-30) cc_final: 0.8057 (m-30) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.4378 time to fit residues: 112.7738 Evaluate side-chains 158 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1587 GLU Chi-restraints excluded: chain B residue 1634 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 53 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 195 optimal weight: 50.0000 chunk 202 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 162 optimal weight: 0.0010 chunk 91 optimal weight: 7.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 ASN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098296 restraints weight = 89683.082| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.68 r_work: 0.3198 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21393 Z= 0.223 Angle : 0.657 12.465 29016 Z= 0.334 Chirality : 0.044 0.321 3163 Planarity : 0.005 0.066 3599 Dihedral : 13.340 173.820 3324 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Rotamer: Outliers : 1.42 % Allowed : 11.54 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.17), residues: 2497 helix: 1.67 (0.18), residues: 902 sheet: -0.50 (0.31), residues: 318 loop : -1.99 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 375 HIS 0.005 0.001 HIS B1610 PHE 0.021 0.002 PHE B 201 TYR 0.021 0.002 TYR A 685 ARG 0.007 0.001 ARG B1503 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 751) hydrogen bonds : angle 4.40821 ( 2157) metal coordination : bond 0.01327 ( 16) metal coordination : angle 2.47945 ( 21) covalent geometry : bond 0.00524 (21377) covalent geometry : angle 0.65418 (28995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: A 492 LYS cc_start: 0.8100 (tppt) cc_final: 0.7596 (tptp) REVERT: A 661 LYS cc_start: 0.7347 (pttp) cc_final: 0.6809 (mmmt) REVERT: A 751 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7492 (mm) REVERT: B 394 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7746 (t80) REVERT: B 440 LYS cc_start: 0.8745 (tptt) cc_final: 0.8500 (tptp) REVERT: B 510 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6976 (p) REVERT: B 531 GLU cc_start: 0.8649 (mp0) cc_final: 0.7810 (mp0) REVERT: B 647 ASP cc_start: 0.7625 (m-30) cc_final: 0.7198 (m-30) REVERT: B 895 MET cc_start: 0.6687 (tpt) cc_final: 0.6456 (tpt) REVERT: B 1437 PHE cc_start: 0.8221 (t80) cc_final: 0.7888 (t80) REVERT: B 1438 LYS cc_start: 0.7381 (mmtt) cc_final: 0.6919 (mmtm) REVERT: B 1471 ASP cc_start: 0.7295 (m-30) cc_final: 0.6911 (m-30) REVERT: B 1487 ILE cc_start: 0.6613 (mt) cc_final: 0.6342 (mt) REVERT: B 1525 GLN cc_start: 0.7211 (tp-100) cc_final: 0.6934 (tp40) REVERT: B 1587 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: B 1627 ASP cc_start: 0.8413 (m-30) cc_final: 0.8111 (m-30) REVERT: B 1788 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.5910 (p90) outliers start: 28 outliers final: 17 residues processed: 153 average time/residue: 0.3679 time to fit residues: 88.1391 Evaluate side-chains 154 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1587 GLU Chi-restraints excluded: chain B residue 1634 THR Chi-restraints excluded: chain B residue 1788 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 93 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 217 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102008 restraints weight = 74149.584| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.71 r_work: 0.3259 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21393 Z= 0.120 Angle : 0.576 12.314 29016 Z= 0.291 Chirality : 0.041 0.293 3163 Planarity : 0.004 0.061 3599 Dihedral : 13.165 172.687 3324 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.22 % Favored : 92.30 % Rotamer: Outliers : 1.28 % Allowed : 11.82 % Favored : 86.89 % 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: -0.36 (0.17), residues: 2497 helix: 1.86 (0.18), residues: 899 sheet: -0.35 (0.31), residues: 313 loop : -1.86 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 375 HIS 0.003 0.001 HIS B1610 PHE 0.019 0.001 PHE B 201 TYR 0.016 0.001 TYR A 685 ARG 0.004 0.000 ARG B1777 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 751) hydrogen bonds : angle 4.16595 ( 2157) metal coordination : bond 0.00805 ( 16) metal coordination : angle 2.35454 ( 21) covalent geometry : bond 0.00271 (21377) covalent geometry : angle 0.57303 (28995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 2.493 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 352 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: A 492 LYS cc_start: 0.7952 (tppt) cc_final: 0.7748 (tppt) REVERT: A 661 LYS cc_start: 0.7242 (pttp) cc_final: 0.6677 (tttm) REVERT: A 751 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7422 (mm) REVERT: B 343 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6656 (pp) REVERT: B 394 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7733 (t80) REVERT: B 440 LYS cc_start: 0.8698 (tptt) cc_final: 0.8326 (mmtt) REVERT: B 510 CYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6783 (p) REVERT: B 531 GLU cc_start: 0.8743 (mp0) cc_final: 0.7929 (mp0) REVERT: B 647 ASP cc_start: 0.7507 (m-30) cc_final: 0.7013 (m-30) REVERT: B 895 MET cc_start: 0.6705 (tpt) cc_final: 0.6470 (tpt) REVERT: B 1437 PHE cc_start: 0.8179 (t80) cc_final: 0.7906 (t80) REVERT: B 1438 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6898 (mmtm) REVERT: B 1471 ASP cc_start: 0.7277 (m-30) cc_final: 0.6938 (m-30) REVERT: B 1525 GLN cc_start: 0.7099 (tp-100) cc_final: 0.6828 (tp40) REVERT: B 1587 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: B 1627 ASP cc_start: 0.8414 (m-30) cc_final: 0.8151 (m-30) REVERT: B 1788 TRP cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (p-90) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.3467 time to fit residues: 85.5510 Evaluate side-chains 160 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1587 GLU Chi-restraints excluded: chain B residue 1634 THR Chi-restraints excluded: chain B residue 1788 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 197 optimal weight: 0.0170 chunk 121 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 204 optimal weight: 30.0000 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 400 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.143679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104887 restraints weight = 71852.826| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.30 r_work: 0.3319 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21393 Z= 0.100 Angle : 0.548 12.548 29016 Z= 0.275 Chirality : 0.040 0.313 3163 Planarity : 0.004 0.060 3599 Dihedral : 12.922 172.266 3324 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.58 % Favored : 91.94 % Rotamer: Outliers : 1.14 % Allowed : 12.11 % Favored : 86.75 % 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: -0.16 (0.17), residues: 2497 helix: 1.99 (0.18), residues: 900 sheet: -0.10 (0.32), residues: 310 loop : -1.75 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 375 HIS 0.003 0.000 HIS A 146 PHE 0.025 0.001 PHE A 652 TYR 0.012 0.001 TYR A 685 ARG 0.004 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 751) hydrogen bonds : angle 4.00732 ( 2157) metal coordination : bond 0.00433 ( 16) metal coordination : angle 2.33669 ( 21) covalent geometry : bond 0.00216 (21377) covalent geometry : angle 0.54425 (28995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 352 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 661 LYS cc_start: 0.6646 (pttp) cc_final: 0.6242 (tttm) REVERT: A 751 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7456 (mm) REVERT: B 325 LEU cc_start: 0.8306 (mm) cc_final: 0.7925 (mm) REVERT: B 343 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6641 (pp) REVERT: B 394 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 440 LYS cc_start: 0.8652 (tptt) cc_final: 0.8277 (mmtt) REVERT: B 510 CYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6519 (p) REVERT: B 531 GLU cc_start: 0.8821 (mp0) cc_final: 0.8036 (mp0) REVERT: B 647 ASP cc_start: 0.7590 (m-30) cc_final: 0.7118 (m-30) REVERT: B 895 MET cc_start: 0.6727 (tpt) cc_final: 0.6486 (tpt) REVERT: B 1438 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6810 (mmtm) REVERT: B 1471 ASP cc_start: 0.7443 (m-30) cc_final: 0.7185 (m-30) REVERT: B 1525 GLN cc_start: 0.6948 (tp-100) cc_final: 0.6748 (tp40) REVERT: B 1627 ASP cc_start: 0.8425 (m-30) cc_final: 0.8163 (m-30) REVERT: B 1788 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.8248 (p-90) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 0.3623 time to fit residues: 95.5158 Evaluate side-chains 165 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1634 THR Chi-restraints excluded: chain B residue 1788 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 196 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 250 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 219 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 224 optimal weight: 0.0980 chunk 221 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 ASN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105460 restraints weight = 71966.675| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.46 r_work: 0.3329 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21393 Z= 0.096 Angle : 0.546 12.474 29016 Z= 0.274 Chirality : 0.039 0.318 3163 Planarity : 0.004 0.061 3599 Dihedral : 12.796 170.835 3324 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.66 % Favored : 92.86 % Rotamer: Outliers : 1.09 % Allowed : 12.16 % Favored : 86.75 % 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: -0.06 (0.17), residues: 2497 helix: 2.06 (0.18), residues: 899 sheet: -0.05 (0.32), residues: 294 loop : -1.65 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 375 HIS 0.003 0.000 HIS A 146 PHE 0.015 0.001 PHE B 201 TYR 0.016 0.001 TYR A 685 ARG 0.004 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 751) hydrogen bonds : angle 3.93983 ( 2157) metal coordination : bond 0.00405 ( 16) metal coordination : angle 2.27425 ( 21) covalent geometry : bond 0.00207 (21377) covalent geometry : angle 0.54244 (28995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13501.73 seconds wall clock time: 234 minutes 28.65 seconds (14068.65 seconds total)