Starting phenix.real_space_refine on Sun Sep 13 06:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_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_14848/09_2026/7zoq_14848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zoq_14848/09_2026/7zoq_14848.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.26s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1} 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: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1} 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: {'RNAv2': 39} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 3, 'rna3p_pyr': 12} Link IDs: {'rna2p': 22, 'rna3p': 16} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 6.54, per 1000 atoms: 0.31 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: 1.65 Conformation dependent library (CDL) restraints added in 1.3 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: 2.29 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: 4.26 Time building geometry restraints manager: 2.12 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: 28732 3.20 - 6.39: 237 6.39 - 9.59: 23 9.59 - 12.79: 2 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 - 32.50: 12426 32.50 - 64.99: 479 64.99 - 97.49: 50 97.49 - 129.98: 0 129.98 - 162.48: 1 Dihedral angle restraints: 12956 sinusoidal: 5619 harmonic: 7337 Sorted by residual: dihedral pdb=" C4' C C 20 " pdb=" C3' C C 20 " pdb=" C2' C C 20 " pdb=" C1' C C 20 " ideal model delta sinusoidal sigma weight residual 36.34 -39.87 76.21 1 3.10e+00 1.04e-01 7.61e+02 dihedral pdb=" C4' U C 27 " pdb=" C3' U C 27 " pdb=" C2' U C 27 " pdb=" C1' U C 27 " ideal model delta sinusoidal sigma weight residual 36.34 -38.71 75.05 1 3.10e+00 1.04e-01 7.41e+02 dihedral pdb=" C4' A C 26 " pdb=" C3' A C 26 " pdb=" C2' A C 26 " pdb=" C1' A C 26 " ideal model delta sinusoidal sigma weight residual 36.35 -38.68 75.02 1 3.10e+00 1.04e-01 7.41e+02 ... (remaining 12953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2917 0.102 - 0.203: 165 0.203 - 0.305: 75 0.305 - 0.407: 4 0.407 - 0.508: 2 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=" P G C 21 " pdb=" OP1 G C 21 " pdb=" OP2 G C 21 " pdb=" O5' G C 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C3' U C 27 " pdb=" C4' U C 27 " pdb=" O3' U C 27 " pdb=" C2' U C 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 3.94e+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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.850 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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= 0.198 Angle : 0.710 15.983 29016 Z= 0.412 Chirality : 0.061 0.508 3163 Planarity : 0.005 0.119 3599 Dihedral : 16.667 162.478 8200 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.87 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (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 ARG 0.006 0.000 ARG B 786 TYR 0.019 0.001 TYR B1444 PHE 0.017 0.001 PHE B 201 TRP 0.012 0.001 TRP B1788 HIS 0.007 0.001 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.20 (21377) covalent geometry : angle 0.70728 / 0.41 (28995) hydrogen bonds : bond 0.16015 / 10.79 ( 751) hydrogen bonds : angle 5.70734 / 4.14 ( 2157) metal coordination : bond 0.00565 / 0.37 ( 16) metal coordination : angle 2.32482 / 1.48 ( 21) *********************** 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 : 0.689 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: 0.1523 time to fit residues: 45.3780 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 : 0.697 ------------------------------------------------------------------------------- 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 216 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104328 restraints weight = 70690.096| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.96 r_work: 0.3320 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21393 Z= 0.183 Angle : 0.866 20.962 29016 Z= 0.387 Chirality : 0.081 1.204 3163 Planarity : 0.005 0.086 3599 Dihedral : 11.783 155.639 3208 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.14 % Favored : 91.34 % Rotamer: Outliers : 0.85 % Allowed : 5.84 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2497 helix: 2.07 (0.18), residues: 903 sheet: -0.05 (0.31), residues: 308 loop : -1.67 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1777 TYR 0.018 0.002 TYR A 766 PHE 0.024 0.001 PHE B 201 TRP 0.015 0.001 TRP B1788 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (21377) covalent geometry : angle 0.86399 / 0.39 (28995) hydrogen bonds : bond 0.04568 / 3.03 ( 751) hydrogen bonds : angle 4.58382 / 3.35 ( 2157) metal coordination : bond 0.01255 / 0.81 ( 16) metal coordination : angle 2.18148 / 1.44 ( 21) *********************** 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 153 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.711 Fit side-chains REVERT: A 492 LYS cc_start: 0.7887 (tppt) cc_final: 0.7551 (tptt) REVERT: A 532 ASP cc_start: 0.7619 (m-30) cc_final: 0.7406 (m-30) REVERT: B 394 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7748 (t80) REVERT: B 395 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8250 (mm) REVERT: B 1414 ARG cc_start: 0.4843 (mmp-170) cc_final: 0.4465 (mmm160) REVERT: B 1430 GLN cc_start: 0.7830 (tp40) cc_final: 0.7481 (mm110) REVERT: B 1442 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8064 (pm20) outliers start: 16 outliers final: 8 residues processed: 149 average time/residue: 0.1413 time to fit residues: 33.3079 Evaluate side-chains 143 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1442 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 186 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 164 optimal weight: 0.0670 chunk 178 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 overall best weight: 3.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 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 = 0.4000 r_free = 0.4000 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103633 restraints weight = 57055.357| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.84 r_work: 0.3290 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21393 Z= 0.197 Angle : 0.763 12.293 29016 Z= 0.360 Chirality : 0.065 0.825 3163 Planarity : 0.005 0.076 3599 Dihedral : 12.539 169.165 3192 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.42 % Favored : 91.02 % Rotamer: Outliers : 1.14 % Allowed : 7.98 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2497 helix: 1.88 (0.18), residues: 902 sheet: -0.20 (0.32), residues: 303 loop : -1.82 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1777 TYR 0.016 0.002 TYR A 685 PHE 0.026 0.002 PHE B 201 TRP 0.021 0.001 TRP B1788 HIS 0.005 0.001 HIS B1610 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (21377) covalent geometry : angle 0.76045 / 0.36 (28995) hydrogen bonds : bond 0.04824 / 3.20 ( 751) hydrogen bonds : angle 4.43553 / 3.23 ( 2157) metal coordination : bond 0.01523 / 0.98 ( 16) metal coordination : angle 2.48053 / 1.76 ( 21) *********************** 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 163 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.692 Fit side-chains REVERT: A 164 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 492 LYS cc_start: 0.7901 (tppt) cc_final: 0.7482 (tptt) REVERT: A 532 ASP cc_start: 0.7736 (m-30) cc_final: 0.7528 (m-30) REVERT: B 325 LEU cc_start: 0.8297 (mm) cc_final: 0.7940 (mm) REVERT: B 394 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7706 (t80) REVERT: B 647 ASP cc_start: 0.7669 (m-30) cc_final: 0.7374 (m-30) REVERT: B 770 ASN cc_start: 0.8760 (m-40) cc_final: 0.8521 (m-40) REVERT: B 895 MET cc_start: 0.6482 (tpt) cc_final: 0.6161 (tpt) REVERT: B 1457 PHE cc_start: 0.6391 (t80) cc_final: 0.6186 (t80) REVERT: B 1471 ASP cc_start: 0.7034 (m-30) cc_final: 0.6655 (m-30) outliers start: 22 outliers final: 14 residues processed: 156 average time/residue: 0.1610 time to fit residues: 38.4332 Evaluate side-chains 148 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 378 SER 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 479 LEU Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1483 THR Chi-restraints excluded: chain B residue 1634 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 229 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS ** 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 = 0.4018 r_free = 0.4018 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102574 restraints weight = 85562.455| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.33 r_work: 0.3283 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21393 Z= 0.145 Angle : 0.694 11.424 29016 Z= 0.325 Chirality : 0.061 0.777 3163 Planarity : 0.004 0.069 3599 Dihedral : 12.294 169.125 3188 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.98 % Favored : 91.46 % Rotamer: Outliers : 1.33 % Allowed : 8.74 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2497 helix: 1.92 (0.18), residues: 901 sheet: -0.27 (0.32), residues: 301 loop : -1.80 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1777 TYR 0.014 0.001 TYR A 685 PHE 0.022 0.001 PHE B 201 TRP 0.016 0.001 TRP B1788 HIS 0.004 0.001 HIS B1371 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (21377) covalent geometry : angle 0.69134 / 0.33 (28995) hydrogen bonds : bond 0.04005 / 2.65 ( 751) hydrogen bonds : angle 4.24196 / 3.09 ( 2157) metal coordination : bond 0.00903 / 0.59 ( 16) metal coordination : angle 2.30747 / 1.65 ( 21) *********************** 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 170 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: A 492 LYS cc_start: 0.7936 (tppt) cc_final: 0.7554 (tptt) REVERT: A 788 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6917 (mptt) REVERT: B 325 LEU cc_start: 0.8352 (mm) cc_final: 0.8009 (mm) REVERT: B 394 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7725 (t80) REVERT: B 510 CYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6739 (p) REVERT: B 531 GLU cc_start: 0.8648 (mp0) cc_final: 0.7919 (mp0) REVERT: B 647 ASP cc_start: 0.7638 (m-30) cc_final: 0.7098 (m-30) REVERT: B 770 ASN cc_start: 0.8814 (m-40) cc_final: 0.8548 (m-40) REVERT: B 793 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 895 MET cc_start: 0.6558 (tpt) cc_final: 0.6170 (tpt) REVERT: B 1457 PHE cc_start: 0.6246 (t80) cc_final: 0.5970 (t80) REVERT: B 1471 ASP cc_start: 0.7127 (m-30) cc_final: 0.6790 (m-30) outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 0.1564 time to fit residues: 39.1848 Evaluate side-chains 153 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 230 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 378 SER 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 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 793 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 130 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104233 restraints weight = 59851.571| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.93 r_work: 0.3311 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 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 = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21393 Z= 0.146 Angle : 0.687 10.916 29016 Z= 0.324 Chirality : 0.059 0.719 3163 Planarity : 0.004 0.065 3599 Dihedral : 12.336 169.445 3188 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.62 % Favored : 91.82 % Rotamer: Outliers : 1.28 % Allowed : 9.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2497 helix: 1.91 (0.18), residues: 902 sheet: -0.16 (0.32), residues: 309 loop : -1.82 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1777 TYR 0.015 0.001 TYR A 685 PHE 0.022 0.001 PHE A 652 TRP 0.022 0.001 TRP A 375 HIS 0.003 0.001 HIS B1610 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (21377) covalent geometry : angle 0.68504 / 0.32 (28995) hydrogen bonds : bond 0.03980 / 2.63 ( 751) hydrogen bonds : angle 4.18807 / 3.05 ( 2157) metal coordination : bond 0.01086 / 0.69 ( 16) metal coordination : angle 2.24857 / 1.59 ( 21) *********************** 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 168 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 375 TRP cc_start: 0.7919 (m-10) cc_final: 0.7578 (m-10) REVERT: A 492 LYS cc_start: 0.7915 (tppt) cc_final: 0.7427 (tptp) REVERT: A 788 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6909 (mptt) REVERT: B 394 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 510 CYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6698 (p) REVERT: B 531 GLU cc_start: 0.8697 (mp0) cc_final: 0.7811 (mp0) REVERT: B 770 ASN cc_start: 0.8747 (m-40) cc_final: 0.8454 (m-40) REVERT: B 895 MET cc_start: 0.6559 (tpt) cc_final: 0.6166 (tpt) REVERT: B 1438 LYS cc_start: 0.7419 (mmtt) cc_final: 0.7027 (mmtm) REVERT: B 1457 PHE cc_start: 0.6113 (t80) cc_final: 0.5742 (t80) REVERT: B 1471 ASP cc_start: 0.7127 (m-30) cc_final: 0.6791 (m-30) REVERT: B 1525 GLN cc_start: 0.6689 (tp40) cc_final: 0.6471 (tp40) outliers start: 25 outliers final: 18 residues processed: 160 average time/residue: 0.1576 time to fit residues: 39.3165 Evaluate side-chains 157 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 192 CYS 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 378 SER 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 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 1519 ILE 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 245 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 694 ASN A 818 GLN B 132 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 400 GLN ** B1540 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098737 restraints weight = 74345.134| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.96 r_work: 0.3234 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21393 Z= 0.273 Angle : 0.820 14.377 29016 Z= 0.391 Chirality : 0.069 0.846 3163 Planarity : 0.005 0.065 3599 Dihedral : 12.652 176.577 3188 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.02 % Favored : 90.46 % Rotamer: Outliers : 1.71 % Allowed : 10.49 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2497 helix: 1.55 (0.18), residues: 901 sheet: -0.58 (0.31), residues: 321 loop : -2.02 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1777 TYR 0.019 0.002 TYR A 685 PHE 0.023 0.002 PHE B 808 TRP 0.022 0.002 TRP B1788 HIS 0.006 0.002 HIS B1272 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (21377) covalent geometry : angle 0.81718 / 0.39 (28995) hydrogen bonds : bond 0.05531 / 3.66 ( 751) hydrogen bonds : angle 4.55340 / 3.31 ( 2157) metal coordination : bond 0.01743 / 1.11 ( 16) metal coordination : angle 2.78482 / 1.99 ( 21) *********************** 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 170 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 375 TRP cc_start: 0.8138 (m100) cc_final: 0.7790 (m-10) REVERT: A 492 LYS cc_start: 0.8060 (tppt) cc_final: 0.7567 (tptp) REVERT: A 661 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6881 (mmmt) REVERT: A 662 LYS cc_start: 0.8273 (mppt) cc_final: 0.7923 (mptt) REVERT: A 732 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 751 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7513 (mm) REVERT: B 394 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7772 (t80) REVERT: B 510 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6996 (p) REVERT: B 647 ASP cc_start: 0.7549 (m-30) cc_final: 0.7121 (m-30) REVERT: B 770 ASN cc_start: 0.8888 (m-40) cc_final: 0.8628 (m-40) REVERT: B 895 MET cc_start: 0.6669 (tpt) cc_final: 0.6417 (tpt) REVERT: B 1437 PHE cc_start: 0.8252 (t80) cc_final: 0.7925 (t80) REVERT: B 1438 LYS cc_start: 0.7381 (mmtt) cc_final: 0.6928 (mmtm) REVERT: B 1471 ASP cc_start: 0.7247 (m-30) cc_final: 0.6885 (m-30) REVERT: B 1487 ILE cc_start: 0.6814 (mt) cc_final: 0.6528 (mt) REVERT: B 1525 GLN cc_start: 0.7038 (tp40) cc_final: 0.6778 (tp40) REVERT: B 1788 TRP cc_start: 0.8652 (OUTLIER) cc_final: 0.5896 (p90) outliers start: 34 outliers final: 21 residues processed: 160 average time/residue: 0.1482 time to fit residues: 37.5147 Evaluate side-chains 158 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 378 SER Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 351 ILE 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 1380 THR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1528 ILE Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1634 THR Chi-restraints excluded: chain B residue 1788 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 195 optimal weight: 0.5980 chunk 5 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4006 r_free = 0.4006 target = 0.141589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102209 restraints weight = 76251.535| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.04 r_work: 0.3288 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21393 Z= 0.136 Angle : 0.695 11.825 29016 Z= 0.327 Chirality : 0.060 0.779 3163 Planarity : 0.004 0.075 3599 Dihedral : 12.532 172.974 3188 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.34 % Favored : 92.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2497 helix: 1.79 (0.18), residues: 902 sheet: -0.31 (0.32), residues: 306 loop : -1.96 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1777 TYR 0.017 0.001 TYR A 222 PHE 0.019 0.001 PHE B 201 TRP 0.015 0.001 TRP B1788 HIS 0.003 0.001 HIS B1272 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (21377) covalent geometry : angle 0.69181 / 0.33 (28995) hydrogen bonds : bond 0.04007 / 2.64 ( 751) hydrogen bonds : angle 4.24809 / 3.08 ( 2157) metal coordination : bond 0.01028 / 0.66 ( 16) metal coordination : angle 2.43728 / 1.76 ( 21) *********************** 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 170 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 375 TRP cc_start: 0.8067 (m100) cc_final: 0.7800 (m-10) REVERT: A 492 LYS cc_start: 0.8003 (tppt) cc_final: 0.7450 (tptp) REVERT: A 564 GLU cc_start: 0.7891 (tp30) cc_final: 0.7627 (mt-10) REVERT: A 661 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6880 (mmmt) REVERT: A 662 LYS cc_start: 0.8167 (mppt) cc_final: 0.7801 (mptt) REVERT: A 751 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7357 (mm) REVERT: B 394 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7735 (t80) REVERT: B 510 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6745 (p) REVERT: B 531 GLU cc_start: 0.8601 (mp0) cc_final: 0.7833 (mp0) REVERT: B 647 ASP cc_start: 0.7407 (m-30) cc_final: 0.6919 (m-30) REVERT: B 770 ASN cc_start: 0.8826 (m-40) cc_final: 0.8558 (m-40) REVERT: B 895 MET cc_start: 0.6873 (tpt) cc_final: 0.6645 (tpt) REVERT: B 1437 PHE cc_start: 0.8219 (t80) cc_final: 0.7924 (t80) REVERT: B 1438 LYS cc_start: 0.7419 (mmtt) cc_final: 0.6994 (mmtm) REVERT: B 1471 ASP cc_start: 0.7316 (m-30) cc_final: 0.6973 (m-30) REVERT: B 1525 GLN cc_start: 0.6987 (tp40) cc_final: 0.6777 (tp40) REVERT: B 1587 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: B 1627 ASP cc_start: 0.8427 (m-30) cc_final: 0.8145 (m-30) outliers start: 28 outliers final: 15 residues processed: 162 average time/residue: 0.1494 time to fit residues: 38.0108 Evaluate side-chains 156 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 552 LEU Chi-restraints excluded: chain A residue 661 LYS 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 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 1412 THR Chi-restraints excluded: chain B residue 1519 ILE Chi-restraints excluded: chain B residue 1528 ILE 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 194 optimal weight: 30.0000 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 234 optimal weight: 0.3980 chunk 137 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 694 ASN B 400 GLN B1525 GLN ** B1540 HIS ** 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 = 0.4020 r_free = 0.4020 target = 0.142693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105629 restraints weight = 50590.467| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.68 r_work: 0.3335 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 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 = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21393 Z= 0.126 Angle : 0.670 12.525 29016 Z= 0.315 Chirality : 0.057 0.695 3163 Planarity : 0.004 0.063 3599 Dihedral : 12.368 171.767 3188 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.66 % Favored : 91.86 % Rotamer: Outliers : 1.23 % Allowed : 12.11 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2497 helix: 1.90 (0.18), residues: 898 sheet: -0.29 (0.31), residues: 313 loop : -1.85 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1777 TYR 0.012 0.001 TYR A 222 PHE 0.019 0.001 PHE B 201 TRP 0.013 0.001 TRP B1661 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (21377) covalent geometry : angle 0.66769 / 0.32 (28995) hydrogen bonds : bond 0.03663 / 2.43 ( 751) hydrogen bonds : angle 4.12163 / 2.99 ( 2157) metal coordination : bond 0.00574 / 0.37 ( 16) metal coordination : angle 2.24942 / 1.57 ( 21) *********************** 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 169 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 352 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: A 375 TRP cc_start: 0.7972 (m100) cc_final: 0.7707 (m-10) REVERT: A 564 GLU cc_start: 0.7901 (tp30) cc_final: 0.7615 (mt-10) REVERT: A 661 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6574 (tttm) REVERT: A 662 LYS cc_start: 0.8006 (mppt) cc_final: 0.7624 (mptt) REVERT: A 751 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7294 (mm) REVERT: B 343 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6676 (pp) REVERT: B 394 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 440 LYS cc_start: 0.8620 (tptt) cc_final: 0.8181 (mmtt) REVERT: B 510 CYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6685 (p) REVERT: B 531 GLU cc_start: 0.8689 (mp0) cc_final: 0.7856 (mp0) REVERT: B 647 ASP cc_start: 0.7374 (m-30) cc_final: 0.6887 (m-30) REVERT: B 770 ASN cc_start: 0.8801 (m-40) cc_final: 0.8518 (m-40) REVERT: B 895 MET cc_start: 0.6821 (tpt) cc_final: 0.6524 (tpt) REVERT: B 1437 PHE cc_start: 0.8185 (t80) cc_final: 0.7925 (t80) REVERT: B 1438 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6900 (mmtm) REVERT: B 1471 ASP cc_start: 0.7279 (m-30) cc_final: 0.6960 (m-30) REVERT: B 1525 GLN cc_start: 0.7027 (tp-100) cc_final: 0.6748 (tp40) REVERT: B 1587 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6182 (pp20) REVERT: B 1627 ASP cc_start: 0.8423 (m-30) cc_final: 0.8145 (m-30) REVERT: B 1788 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.8233 (p-90) outliers start: 24 outliers final: 11 residues processed: 162 average time/residue: 0.1501 time to fit residues: 37.8125 Evaluate side-chains 163 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 661 LYS 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 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 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR 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 17 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 0.0060 chunk 9 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN B 159 ASN B1447 ASN ** B1540 HIS ** 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 = 0.3991 r_free = 0.3991 target = 0.140525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100946 restraints weight = 80112.490| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.09 r_work: 0.3266 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21393 Z= 0.183 Angle : 0.720 12.405 29016 Z= 0.340 Chirality : 0.060 0.696 3163 Planarity : 0.005 0.061 3599 Dihedral : 12.428 170.493 3188 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.58 % Favored : 90.94 % Rotamer: Outliers : 1.57 % Allowed : 11.97 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2497 helix: 1.81 (0.18), residues: 900 sheet: -0.39 (0.31), residues: 314 loop : -1.92 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1777 TYR 0.021 0.001 TYR A 685 PHE 0.018 0.002 PHE B 201 TRP 0.017 0.001 TRP B1788 HIS 0.004 0.001 HIS B1610 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (21377) covalent geometry : angle 0.71760 / 0.34 (28995) hydrogen bonds : bond 0.04405 / 2.92 ( 751) hydrogen bonds : angle 4.25484 / 3.08 ( 2157) metal coordination : bond 0.01224 / 0.77 ( 16) metal coordination : angle 2.25242 / 1.59 ( 21) *********************** 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 172 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: A 352 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 564 GLU cc_start: 0.8091 (tp30) cc_final: 0.7767 (tp30) REVERT: A 661 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6702 (tttm) REVERT: A 662 LYS cc_start: 0.8054 (mppt) cc_final: 0.7666 (mptt) REVERT: A 751 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7505 (mm) REVERT: B 343 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6704 (pp) REVERT: B 394 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7741 (t80) REVERT: B 440 LYS cc_start: 0.8691 (tptt) cc_final: 0.8439 (tptp) REVERT: B 510 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6871 (p) REVERT: B 531 GLU cc_start: 0.8706 (mp0) cc_final: 0.7810 (mp0) REVERT: B 647 ASP cc_start: 0.7562 (m-30) cc_final: 0.7117 (m-30) REVERT: B 770 ASN cc_start: 0.8839 (m-40) cc_final: 0.8572 (m-40) REVERT: B 895 MET cc_start: 0.6893 (tpt) cc_final: 0.6598 (tpt) REVERT: B 1437 PHE cc_start: 0.8135 (t80) cc_final: 0.7887 (t80) REVERT: B 1438 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6838 (mmtm) REVERT: B 1471 ASP cc_start: 0.7345 (m-30) cc_final: 0.7009 (m-30) REVERT: B 1525 GLN cc_start: 0.7089 (tp-100) cc_final: 0.6817 (tp40) REVERT: B 1587 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6183 (pp20) REVERT: B 1627 ASP cc_start: 0.8417 (m-30) cc_final: 0.8163 (m-30) REVERT: B 1788 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.8157 (p-90) outliers start: 31 outliers final: 18 residues processed: 163 average time/residue: 0.1490 time to fit residues: 38.0423 Evaluate side-chains 163 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE 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 352 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 661 LYS 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 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1528 ILE 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 102 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4001 r_free = 0.4001 target = 0.141296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102183 restraints weight = 66741.740| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.74 r_work: 0.3297 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21393 Z= 0.156 Angle : 0.701 12.330 29016 Z= 0.331 Chirality : 0.059 0.713 3163 Planarity : 0.004 0.062 3599 Dihedral : 12.430 170.798 3188 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.14 % Favored : 91.38 % Rotamer: Outliers : 1.28 % Allowed : 12.20 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2497 helix: 1.88 (0.18), residues: 893 sheet: -0.34 (0.32), residues: 309 loop : -1.88 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1777 TYR 0.020 0.001 TYR A 685 PHE 0.019 0.001 PHE B 201 TRP 0.056 0.001 TRP A 375 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (21377) covalent geometry : angle 0.69858 / 0.33 (28995) hydrogen bonds : bond 0.04130 / 2.74 ( 751) hydrogen bonds : angle 4.22330 / 3.06 ( 2157) metal coordination : bond 0.00946 / 0.61 ( 16) metal coordination : angle 2.26949 / 1.63 ( 21) ********************** 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 163 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: A 352 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: A 564 GLU cc_start: 0.8117 (tp30) cc_final: 0.7778 (tp30) REVERT: A 661 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6678 (tttm) REVERT: A 751 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7543 (mm) REVERT: B 343 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6714 (pp) REVERT: B 394 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 440 LYS cc_start: 0.8724 (tptt) cc_final: 0.8474 (tptp) REVERT: B 510 CYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6688 (p) REVERT: B 531 GLU cc_start: 0.8697 (mp0) cc_final: 0.7803 (mp0) REVERT: B 647 ASP cc_start: 0.7666 (m-30) cc_final: 0.7248 (m-30) REVERT: B 770 ASN cc_start: 0.8839 (m-40) cc_final: 0.8578 (m-40) REVERT: B 895 MET cc_start: 0.7091 (tpt) cc_final: 0.6785 (tpt) REVERT: B 1437 PHE cc_start: 0.8117 (t80) cc_final: 0.7866 (t80) REVERT: B 1438 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6822 (mmtm) REVERT: B 1471 ASP cc_start: 0.7483 (m-30) cc_final: 0.7237 (m-30) REVERT: B 1525 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6845 (tp40) REVERT: B 1587 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6172 (pp20) REVERT: B 1627 ASP cc_start: 0.8469 (m-30) cc_final: 0.8241 (m-30) REVERT: B 1788 TRP cc_start: 0.8613 (OUTLIER) cc_final: 0.8208 (p-90) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 0.1519 time to fit residues: 37.7798 Evaluate side-chains 158 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 352 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 661 LYS 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 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1528 ILE 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 99 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.143445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103926 restraints weight = 83303.653| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.22 r_work: 0.3314 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21393 Z= 0.117 Angle : 0.660 12.197 29016 Z= 0.310 Chirality : 0.055 0.659 3163 Planarity : 0.004 0.061 3599 Dihedral : 12.316 172.148 3188 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.62 % Favored : 91.90 % Rotamer: Outliers : 1.14 % Allowed : 12.25 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2497 helix: 1.96 (0.18), residues: 892 sheet: -0.21 (0.32), residues: 305 loop : -1.79 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1777 TYR 0.017 0.001 TYR A 685 PHE 0.017 0.001 PHE B 201 TRP 0.042 0.001 TRP A 375 HIS 0.003 0.001 HIS B1610 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (21377) covalent geometry : angle 0.65733 / 0.31 (28995) hydrogen bonds : bond 0.03440 / 2.28 ( 751) hydrogen bonds : angle 4.09015 / 2.97 ( 2157) metal coordination : bond 0.00622 / 0.40 ( 16) metal coordination : angle 2.27624 / 1.57 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.46 seconds wall clock time: 103 minutes 54.01 seconds (6234.01 seconds total)