Starting phenix.real_space_refine on Wed Mar 4 12:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.map" model { file = "/net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wah_32385/03_2026/7wah_32385.cif" } resolution = 2.45 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= -0.006 sd= 0.105 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 61 5.49 5 S 56 5.16 5 C 8130 2.51 5 N 2348 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13217 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 17} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "A" Number of atoms: 11895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11895 Classifications: {'peptide': 1473} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 80, 'TRANS': 1392} Chain breaks: 9 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" 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 2022 SG CYS A 86 48.068 76.770 17.624 1.00 74.00 S ATOM 2268 SG CYS A 115 48.227 74.846 14.354 1.00 96.17 S ATOM 2330 SG CYS A 123 50.567 73.956 17.218 1.00 70.51 S ATOM 2354 SG CYS A 126 46.859 73.185 17.504 1.00 60.85 S ATOM 4438 SG CYS A 463 42.328 90.654 47.896 1.00 71.44 S ATOM 4500 SG CYS A 472 42.013 91.085 44.076 1.00 57.69 S ATOM 4514 SG CYS A 474 45.077 92.311 45.949 1.00 59.04 S ATOM 4536 SG CYS A 477 44.492 88.593 45.583 1.00 60.88 S ATOM 6350 SG CYS A 706 31.561 96.931 73.123 1.00 95.71 S ATOM 6365 SG CYS A 708 34.219 98.389 75.450 1.00 77.27 S ATOM 6387 SG CYS A 711 35.034 95.356 73.340 1.00 74.09 S ATOM 8250 SG CYS A 965 30.141 81.704 108.993 1.00 40.04 S ATOM 11040 SG CYS A1312 28.017 82.679 105.973 1.00 54.59 S ATOM 11103 SG CYS A1342 29.737 85.304 108.209 1.00 31.20 S ATOM 11121 SG CYS A1345 31.771 83.230 105.905 1.00 60.12 S Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13217 At special positions: 0 Unit cell: (84.66, 123.67, 172.64, 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 56 16.00 P 61 15.00 O 2618 8.00 N 2348 7.00 C 8130 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: 1.06 Conformation dependent library (CDL) restraints added in 444.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 472 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " Number of angles added : 21 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 23 sheets defined 28.5% alpha, 29.7% beta 20 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.547A pdb=" N GLY A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.705A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.928A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 5.706A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 343 removed outlier: 3.626A pdb=" N LYS A 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 removed outlier: 3.654A pdb=" N ARG A 598 " --> pdb=" O TRP A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.540A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 649 Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.951A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.579A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1179 through 1183 Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.196A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1426 removed outlier: 4.172A pdb=" N THR A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.737A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 5.027A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 5.027A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 504 removed outlier: 10.417A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.009A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.009A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.535A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB4, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.509A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.676A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.884A pdb=" N ILE A 943 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 6.492A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.105A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.884A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 994 removed outlier: 6.826A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1092 through 1098 removed outlier: 6.348A pdb=" N SER A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A1076 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A1082 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A1122 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A1046 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER A1124 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A1044 " --> pdb=" O SER A1124 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A1126 " --> pdb=" O PHE A1042 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1042 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 19.741A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.425A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 47.243A pdb=" N ILE A1002 " --> pdb=" O CYS A1119 " (cutoff:3.500A) removed outlier: 40.819A pdb=" N VAL A1121 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 34.447A pdb=" N LYS A1004 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 27.522A pdb=" N ASP A1123 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 22.294A pdb=" N SER A1006 " --> pdb=" O ASP A1123 " (cutoff:3.500A) removed outlier: 16.384A pdb=" N ARG A1125 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 13.328A pdb=" N THR A1008 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN A1127 " --> pdb=" O THR A1008 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 7.316A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4055 1.34 - 1.46: 2665 1.46 - 1.58: 6730 1.58 - 1.70: 121 1.70 - 1.82: 80 Bond restraints: 13651 Sorted by residual: bond pdb=" N PRO A1138 " pdb=" CA PRO A1138 " ideal model delta sigma weight residual 1.468 1.479 -0.011 7.90e-03 1.60e+04 2.04e+00 bond pdb=" CA GLU A1196 " pdb=" CB GLU A1196 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.17e+00 bond pdb=" N PRO A1153 " pdb=" CA PRO A1153 " ideal model delta sigma weight residual 1.469 1.481 -0.013 1.28e-02 6.10e+03 9.94e-01 bond pdb=" N ASP A1315 " pdb=" CA ASP A1315 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.72e-01 bond pdb=" CB PRO A1368 " pdb=" CG PRO A1368 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.51e-01 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 17768 1.02 - 2.05: 740 2.05 - 3.07: 146 3.07 - 4.09: 36 4.09 - 5.12: 6 Bond angle restraints: 18696 Sorted by residual: angle pdb=" C2' U R 1 " pdb=" C1' U R 1 " pdb=" N1 U R 1 " ideal model delta sigma weight residual 112.00 117.12 -5.12 1.50e+00 4.44e-01 1.16e+01 angle pdb=" O4' G R 19 " pdb=" C1' G R 19 " pdb=" N9 G R 19 " ideal model delta sigma weight residual 108.20 113.04 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N ILE A1424 " pdb=" CA ILE A1424 " pdb=" C ILE A1424 " ideal model delta sigma weight residual 112.80 109.62 3.18 1.15e+00 7.56e-01 7.65e+00 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 114.66 111.27 3.39 1.24e+00 6.50e-01 7.46e+00 angle pdb=" N GLY A 641 " pdb=" CA GLY A 641 " pdb=" C GLY A 641 " ideal model delta sigma weight residual 112.14 115.47 -3.33 1.29e+00 6.01e-01 6.66e+00 ... (remaining 18691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 7888 23.25 - 46.51: 290 46.51 - 69.76: 118 69.76 - 93.01: 19 93.01 - 116.27: 2 Dihedral angle restraints: 8317 sinusoidal: 4076 harmonic: 4241 Sorted by residual: dihedral pdb=" O4' A R 38 " pdb=" C1' A R 38 " pdb=" N9 A R 38 " pdb=" C4 A R 38 " ideal model delta sinusoidal sigma weight residual 68.00 137.16 -69.16 1 1.70e+01 3.46e-03 2.14e+01 dihedral pdb=" CA ASN A 640 " pdb=" C ASN A 640 " pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta harmonic sigma weight residual 180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" O4' A R 12 " pdb=" C1' A R 12 " pdb=" N9 A R 12 " pdb=" C4 A R 12 " ideal model delta sinusoidal sigma weight residual -106.00 -156.28 50.28 1 1.70e+01 3.46e-03 1.20e+01 ... (remaining 8314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1667 0.049 - 0.099: 278 0.099 - 0.148: 63 0.148 - 0.197: 0 0.197 - 0.247: 2 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1' G R 19 " pdb=" O4' G R 19 " pdb=" C2' G R 19 " pdb=" N9 G R 19 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' U R 1 " pdb=" O4' U R 1 " pdb=" C2' U R 1 " pdb=" N1 U R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A 628 " pdb=" N ILE A 628 " pdb=" C ILE A 628 " pdb=" CB ILE A 628 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2007 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U R 1 " 0.038 2.00e-02 2.50e+03 1.98e-02 8.78e+00 pdb=" N1 U R 1 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U R 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U R 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U R 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U R 1 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U R 1 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U R 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U R 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO A 904 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G R 19 " 0.028 2.00e-02 2.50e+03 1.33e-02 5.28e+00 pdb=" N9 G R 19 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G R 19 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G R 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G R 19 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G R 19 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G R 19 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G R 19 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G R 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2356 2.77 - 3.30: 12038 3.30 - 3.84: 22979 3.84 - 4.37: 28609 4.37 - 4.90: 46429 Nonbonded interactions: 112411 Sorted by model distance: nonbonded pdb=" OP1 U R 16 " pdb=" OG SER A 564 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A1081 " pdb=" OE1 GLN A1105 " model vdw 2.262 3.040 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.263 3.120 nonbonded pdb=" O ALA A 288 " pdb=" OG SER A 291 " model vdw 2.271 3.040 nonbonded pdb=" OP1 U R 25 " pdb=" OG SER A 948 " model vdw 2.278 3.040 ... (remaining 112406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.190 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.002 0.046 13667 Z= 0.116 Angle : 0.511 5.117 18717 Z= 0.285 Chirality : 0.039 0.247 2010 Planarity : 0.004 0.070 2203 Dihedral : 14.178 116.269 5581 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.55 % Allowed : 3.52 % Favored : 95.94 % 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: 0.28 (0.22), residues: 1453 helix: 0.93 (0.28), residues: 353 sheet: 0.51 (0.29), residues: 290 loop : -0.20 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1356 TYR 0.010 0.001 TYR A1209 PHE 0.017 0.001 PHE A 757 TRP 0.010 0.001 TRP A1600 HIS 0.003 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00229 (13651) covalent geometry : angle 0.50862 (18696) hydrogen bonds : bond 0.16084 ( 470) hydrogen bonds : angle 6.62964 ( 1316) metal coordination : bond 0.01017 ( 16) metal coordination : angle 1.57217 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 28 LYS cc_start: 0.6838 (ttmt) cc_final: 0.6532 (ttpt) REVERT: A 100 GLN cc_start: 0.6771 (mt0) cc_final: 0.6570 (mt0) REVERT: A 158 LYS cc_start: 0.7591 (mmtt) cc_final: 0.5996 (ptpp) REVERT: A 165 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7826 (mttp) REVERT: A 179 LYS cc_start: 0.7538 (tptm) cc_final: 0.7245 (mttp) REVERT: A 209 LYS cc_start: 0.7904 (mttp) cc_final: 0.7542 (mtmp) REVERT: A 277 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7674 (mptt) REVERT: A 423 GLU cc_start: 0.6971 (pt0) cc_final: 0.6678 (pm20) REVERT: A 559 MET cc_start: 0.8379 (mmt) cc_final: 0.8158 (mmt) REVERT: A 577 TYR cc_start: 0.7593 (p90) cc_final: 0.7382 (p90) REVERT: A 611 ASN cc_start: 0.6104 (m110) cc_final: 0.5631 (p0) REVERT: A 692 MET cc_start: 0.5767 (ptm) cc_final: 0.4962 (ttm) REVERT: A 787 GLU cc_start: 0.7719 (pt0) cc_final: 0.6354 (mm-30) REVERT: A 1000 LYS cc_start: 0.7652 (mptt) cc_final: 0.7353 (tmtp) REVERT: A 1041 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7020 (mtp-110) REVERT: A 1132 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6541 (pm20) REVERT: A 1194 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6878 (mmmt) outliers start: 7 outliers final: 4 residues processed: 249 average time/residue: 0.7413 time to fit residues: 197.8728 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 30 ASN A 170 GLN A 184 HIS A 306 HIS A 626 HIS A1018 GLN A1246 ASN A1279 HIS A1476 GLN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154734 restraints weight = 15951.299| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.67 r_work: 0.3735 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13667 Z= 0.137 Angle : 0.551 6.540 18717 Z= 0.295 Chirality : 0.042 0.323 2010 Planarity : 0.005 0.066 2203 Dihedral : 16.173 113.527 2553 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.27 % Allowed : 10.94 % Favored : 86.80 % 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: 0.51 (0.22), residues: 1453 helix: 1.26 (0.28), residues: 349 sheet: 0.36 (0.28), residues: 306 loop : 0.00 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 855 TYR 0.012 0.001 TYR A 591 PHE 0.016 0.002 PHE A1456 TRP 0.011 0.001 TRP A1600 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00299 (13651) covalent geometry : angle 0.54667 (18696) hydrogen bonds : bond 0.04316 ( 470) hydrogen bonds : angle 5.23992 ( 1316) metal coordination : bond 0.00607 ( 16) metal coordination : angle 2.02587 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 28 LYS cc_start: 0.6852 (ttmt) cc_final: 0.6545 (ttpt) REVERT: A 158 LYS cc_start: 0.7688 (mmtt) cc_final: 0.5982 (ptpp) REVERT: A 165 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7852 (mttp) REVERT: A 179 LYS cc_start: 0.7808 (tptm) cc_final: 0.7113 (mttp) REVERT: A 209 LYS cc_start: 0.7983 (mttp) cc_final: 0.7606 (mtmp) REVERT: A 213 GLU cc_start: 0.7889 (mp0) cc_final: 0.7477 (mp0) REVERT: A 423 GLU cc_start: 0.7419 (pt0) cc_final: 0.6928 (pm20) REVERT: A 584 ASP cc_start: 0.7874 (t0) cc_final: 0.7574 (t70) REVERT: A 692 MET cc_start: 0.5851 (ptm) cc_final: 0.4897 (ttp) REVERT: A 787 GLU cc_start: 0.7730 (pt0) cc_final: 0.6378 (mm-30) REVERT: A 798 ASP cc_start: 0.7813 (m-30) cc_final: 0.7510 (m-30) REVERT: A 849 LYS cc_start: 0.6974 (tptp) cc_final: 0.6629 (tmtt) REVERT: A 1000 LYS cc_start: 0.7621 (mptt) cc_final: 0.6986 (tmmm) REVERT: A 1041 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7062 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6819 (tt0) cc_final: 0.6167 (tm130) REVERT: A 1115 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5877 (pp20) REVERT: A 1132 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6616 (pm20) REVERT: A 1194 LYS cc_start: 0.7356 (mmmt) cc_final: 0.7066 (mmmt) REVERT: A 1522 TRP cc_start: 0.6475 (m-10) cc_final: 0.6181 (m-10) outliers start: 29 outliers final: 11 residues processed: 166 average time/residue: 0.7119 time to fit residues: 127.5163 Evaluate side-chains 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A1084 ASN ** A1483 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 = 0.4061 r_free = 0.4061 target = 0.177375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151593 restraints weight = 15988.746| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.66 r_work: 0.3703 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13667 Z= 0.189 Angle : 0.592 6.769 18717 Z= 0.314 Chirality : 0.044 0.334 2010 Planarity : 0.005 0.064 2203 Dihedral : 16.152 112.728 2552 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 12.19 % Favored : 85.08 % 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: 0.33 (0.22), residues: 1453 helix: 1.10 (0.28), residues: 348 sheet: 0.28 (0.27), residues: 321 loop : -0.13 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 967 TYR 0.011 0.002 TYR A1126 PHE 0.021 0.002 PHE A 757 TRP 0.013 0.002 TRP A1600 HIS 0.005 0.001 HIS A1429 Details of bonding type rmsd covalent geometry : bond 0.00425 (13651) covalent geometry : angle 0.58816 (18696) hydrogen bonds : bond 0.04498 ( 470) hydrogen bonds : angle 5.21302 ( 1316) metal coordination : bond 0.00705 ( 16) metal coordination : angle 2.15149 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.310 Fit side-chains REVERT: A 13 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 28 LYS cc_start: 0.6980 (ttmt) cc_final: 0.6570 (ttpt) REVERT: A 47 LYS cc_start: 0.6442 (tmtt) cc_final: 0.5887 (tptp) REVERT: A 108 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5640 (mtt-85) REVERT: A 158 LYS cc_start: 0.7697 (mmtt) cc_final: 0.6001 (ptpp) REVERT: A 165 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7940 (mttp) REVERT: A 179 LYS cc_start: 0.7884 (tptm) cc_final: 0.7324 (mttp) REVERT: A 209 LYS cc_start: 0.7966 (mttp) cc_final: 0.7541 (mtmp) REVERT: A 213 GLU cc_start: 0.7976 (mp0) cc_final: 0.7538 (mp0) REVERT: A 277 LYS cc_start: 0.7942 (mtpm) cc_final: 0.7448 (mptt) REVERT: A 423 GLU cc_start: 0.7386 (pt0) cc_final: 0.6592 (pm20) REVERT: A 572 MET cc_start: 0.7922 (ttp) cc_final: 0.7660 (tmm) REVERT: A 584 ASP cc_start: 0.7920 (t0) cc_final: 0.7596 (t70) REVERT: A 651 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7168 (ptt180) REVERT: A 692 MET cc_start: 0.5835 (ptm) cc_final: 0.4830 (ttp) REVERT: A 787 GLU cc_start: 0.7761 (pt0) cc_final: 0.6386 (mm-30) REVERT: A 849 LYS cc_start: 0.7059 (tptp) cc_final: 0.6709 (tmtt) REVERT: A 1000 LYS cc_start: 0.7631 (mptt) cc_final: 0.6972 (tmmm) REVERT: A 1041 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7087 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5831 (pp20) REVERT: A 1132 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6598 (pm20) REVERT: A 1194 LYS cc_start: 0.7372 (mmmt) cc_final: 0.7086 (mmmt) REVERT: A 1367 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.6226 (p0) outliers start: 35 outliers final: 16 residues processed: 155 average time/residue: 0.7197 time to fit residues: 120.1790 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151871 restraints weight = 15908.530| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.66 r_work: 0.3705 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13667 Z= 0.165 Angle : 0.565 6.616 18717 Z= 0.301 Chirality : 0.043 0.330 2010 Planarity : 0.005 0.062 2203 Dihedral : 16.066 113.100 2551 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 12.73 % Favored : 84.38 % 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: 0.26 (0.22), residues: 1453 helix: 1.04 (0.28), residues: 349 sheet: 0.26 (0.27), residues: 321 loop : -0.18 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 684 TYR 0.011 0.001 TYR A 492 PHE 0.020 0.002 PHE A 757 TRP 0.012 0.001 TRP A1600 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00369 (13651) covalent geometry : angle 0.56105 (18696) hydrogen bonds : bond 0.04107 ( 470) hydrogen bonds : angle 5.09240 ( 1316) metal coordination : bond 0.00534 ( 16) metal coordination : angle 2.02997 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.525 Fit side-chains REVERT: A 13 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 28 LYS cc_start: 0.6903 (ttmt) cc_final: 0.6521 (ttpt) REVERT: A 108 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5618 (mtt-85) REVERT: A 165 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7954 (mttp) REVERT: A 179 LYS cc_start: 0.7872 (tptm) cc_final: 0.7183 (mttp) REVERT: A 209 LYS cc_start: 0.7963 (mttp) cc_final: 0.7410 (mtmm) REVERT: A 213 GLU cc_start: 0.7980 (mp0) cc_final: 0.7585 (mp0) REVERT: A 277 LYS cc_start: 0.7952 (mtpm) cc_final: 0.7433 (mptt) REVERT: A 423 GLU cc_start: 0.7373 (pt0) cc_final: 0.6542 (pm20) REVERT: A 572 MET cc_start: 0.7888 (ttp) cc_final: 0.7631 (tmm) REVERT: A 584 ASP cc_start: 0.7929 (t0) cc_final: 0.7606 (t70) REVERT: A 651 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7168 (ptt180) REVERT: A 692 MET cc_start: 0.5941 (ptm) cc_final: 0.4849 (ttp) REVERT: A 849 LYS cc_start: 0.7060 (tptp) cc_final: 0.6712 (tmtt) REVERT: A 894 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7095 (mmtt) REVERT: A 932 LYS cc_start: 0.6989 (mttm) cc_final: 0.6577 (mtmt) REVERT: A 1000 LYS cc_start: 0.7665 (mptt) cc_final: 0.6935 (tmmm) REVERT: A 1041 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7109 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6814 (tt0) cc_final: 0.6200 (tm130) REVERT: A 1115 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5804 (pp20) REVERT: A 1132 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6518 (pm20) REVERT: A 1367 ASP cc_start: 0.7597 (m-30) cc_final: 0.6222 (p0) outliers start: 37 outliers final: 19 residues processed: 156 average time/residue: 0.7224 time to fit residues: 121.2535 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150849 restraints weight = 16005.590| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.66 r_work: 0.3692 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13667 Z= 0.179 Angle : 0.580 6.726 18717 Z= 0.309 Chirality : 0.044 0.334 2010 Planarity : 0.005 0.061 2203 Dihedral : 16.056 112.885 2551 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.36 % Allowed : 12.66 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.22), residues: 1453 helix: 0.96 (0.28), residues: 349 sheet: 0.18 (0.27), residues: 319 loop : -0.23 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.011 0.002 TYR A 492 PHE 0.022 0.002 PHE A 757 TRP 0.013 0.001 TRP A1600 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00403 (13651) covalent geometry : angle 0.57622 (18696) hydrogen bonds : bond 0.04218 ( 470) hydrogen bonds : angle 5.11740 ( 1316) metal coordination : bond 0.00560 ( 16) metal coordination : angle 2.11256 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.467 Fit side-chains REVERT: A 13 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 28 LYS cc_start: 0.6854 (ttmt) cc_final: 0.6457 (ttpt) REVERT: A 47 LYS cc_start: 0.6347 (tmtt) cc_final: 0.5715 (tptp) REVERT: A 108 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5659 (mtt-85) REVERT: A 158 LYS cc_start: 0.7867 (mptm) cc_final: 0.5977 (ptpp) REVERT: A 165 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7956 (mttp) REVERT: A 179 LYS cc_start: 0.7861 (tptm) cc_final: 0.7314 (mttp) REVERT: A 209 LYS cc_start: 0.7972 (mttp) cc_final: 0.7419 (mtmm) REVERT: A 213 GLU cc_start: 0.8011 (mp0) cc_final: 0.7571 (mp0) REVERT: A 423 GLU cc_start: 0.7328 (pt0) cc_final: 0.6568 (pm20) REVERT: A 572 MET cc_start: 0.7878 (ttp) cc_final: 0.7516 (tmm) REVERT: A 651 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7186 (ptt180) REVERT: A 692 MET cc_start: 0.6031 (ptm) cc_final: 0.5046 (pmt) REVERT: A 849 LYS cc_start: 0.7063 (tptp) cc_final: 0.6719 (tmtt) REVERT: A 894 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7089 (mmtt) REVERT: A 932 LYS cc_start: 0.7056 (mttm) cc_final: 0.6692 (mtmt) REVERT: A 1000 LYS cc_start: 0.7664 (mptt) cc_final: 0.6957 (tmmm) REVERT: A 1041 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7057 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6610 (tt0) cc_final: 0.6061 (tm130) REVERT: A 1115 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5723 (pp20) REVERT: A 1132 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6488 (pm20) REVERT: A 1367 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.6214 (p0) outliers start: 43 outliers final: 22 residues processed: 157 average time/residue: 0.6834 time to fit residues: 115.9315 Evaluate side-chains 156 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1382 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152266 restraints weight = 16040.079| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.66 r_work: 0.3711 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13667 Z= 0.135 Angle : 0.533 6.387 18717 Z= 0.285 Chirality : 0.042 0.321 2010 Planarity : 0.005 0.060 2203 Dihedral : 15.991 113.333 2551 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 13.59 % Favored : 83.52 % 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: 0.26 (0.22), residues: 1453 helix: 1.12 (0.28), residues: 350 sheet: 0.11 (0.27), residues: 323 loop : -0.15 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 684 TYR 0.010 0.001 TYR A 492 PHE 0.017 0.002 PHE A 757 TRP 0.011 0.001 TRP A1600 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00300 (13651) covalent geometry : angle 0.52978 (18696) hydrogen bonds : bond 0.03734 ( 470) hydrogen bonds : angle 4.95864 ( 1316) metal coordination : bond 0.00612 ( 16) metal coordination : angle 1.79382 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.386 Fit side-chains REVERT: A 28 LYS cc_start: 0.6787 (ttmt) cc_final: 0.6416 (ttpt) REVERT: A 47 LYS cc_start: 0.6188 (tmtt) cc_final: 0.5748 (tptp) REVERT: A 108 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5530 (mtt-85) REVERT: A 158 LYS cc_start: 0.7831 (mptm) cc_final: 0.5962 (ptpp) REVERT: A 165 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7941 (mttp) REVERT: A 179 LYS cc_start: 0.7824 (tptm) cc_final: 0.7282 (mttp) REVERT: A 209 LYS cc_start: 0.7998 (mttp) cc_final: 0.7443 (mtmm) REVERT: A 213 GLU cc_start: 0.7997 (mp0) cc_final: 0.7573 (mp0) REVERT: A 277 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7236 (mptt) REVERT: A 423 GLU cc_start: 0.7327 (pt0) cc_final: 0.6574 (pm20) REVERT: A 651 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7083 (ptt180) REVERT: A 692 MET cc_start: 0.5875 (ptm) cc_final: 0.4853 (pmt) REVERT: A 758 ASP cc_start: 0.7793 (m-30) cc_final: 0.7547 (m-30) REVERT: A 798 ASP cc_start: 0.7835 (m-30) cc_final: 0.7552 (m-30) REVERT: A 849 LYS cc_start: 0.6966 (tptp) cc_final: 0.6639 (tmtt) REVERT: A 894 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7107 (mmtt) REVERT: A 932 LYS cc_start: 0.7135 (mttm) cc_final: 0.6729 (mtmt) REVERT: A 1000 LYS cc_start: 0.7658 (mptt) cc_final: 0.6916 (tmmm) REVERT: A 1041 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7028 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6575 (tt0) cc_final: 0.6005 (tm130) REVERT: A 1115 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5725 (pp20) REVERT: A 1131 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 1132 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6444 (pm20) REVERT: A 1367 ASP cc_start: 0.7550 (m-30) cc_final: 0.6360 (p0) outliers start: 37 outliers final: 23 residues processed: 161 average time/residue: 0.7257 time to fit residues: 125.9028 Evaluate side-chains 154 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1483 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 = 0.4076 r_free = 0.4076 target = 0.178977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153560 restraints weight = 16062.277| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.66 r_work: 0.3728 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13667 Z= 0.116 Angle : 0.515 7.721 18717 Z= 0.275 Chirality : 0.041 0.313 2010 Planarity : 0.004 0.059 2203 Dihedral : 15.940 113.435 2551 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.19 % Allowed : 14.69 % Favored : 83.12 % 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: 0.36 (0.22), residues: 1453 helix: 1.24 (0.28), residues: 352 sheet: 0.11 (0.27), residues: 325 loop : -0.07 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 896 TYR 0.010 0.001 TYR A 492 PHE 0.015 0.001 PHE A 757 TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00258 (13651) covalent geometry : angle 0.51222 (18696) hydrogen bonds : bond 0.03461 ( 470) hydrogen bonds : angle 4.80469 ( 1316) metal coordination : bond 0.00382 ( 16) metal coordination : angle 1.74641 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.478 Fit side-chains REVERT: A 28 LYS cc_start: 0.6734 (ttmt) cc_final: 0.6381 (ttpt) REVERT: A 158 LYS cc_start: 0.7814 (mptm) cc_final: 0.5954 (ptpp) REVERT: A 165 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7877 (mttp) REVERT: A 179 LYS cc_start: 0.7887 (tptm) cc_final: 0.7328 (mttp) REVERT: A 209 LYS cc_start: 0.7978 (mttp) cc_final: 0.7453 (mtmm) REVERT: A 213 GLU cc_start: 0.7989 (mp0) cc_final: 0.7524 (mp0) REVERT: A 423 GLU cc_start: 0.7326 (pt0) cc_final: 0.6567 (pm20) REVERT: A 577 TYR cc_start: 0.7578 (p90) cc_final: 0.7318 (p90) REVERT: A 651 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7100 (ptt180) REVERT: A 692 MET cc_start: 0.5971 (ptm) cc_final: 0.5012 (pmt) REVERT: A 798 ASP cc_start: 0.7773 (m-30) cc_final: 0.7477 (m-30) REVERT: A 849 LYS cc_start: 0.6905 (tptp) cc_final: 0.6582 (tmtt) REVERT: A 894 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7109 (mmtt) REVERT: A 932 LYS cc_start: 0.7048 (mttm) cc_final: 0.6636 (mtmt) REVERT: A 1000 LYS cc_start: 0.7620 (mptt) cc_final: 0.6966 (tmmm) REVERT: A 1041 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7037 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5679 (pp20) REVERT: A 1131 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 1132 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6424 (pm20) outliers start: 28 outliers final: 18 residues processed: 147 average time/residue: 0.7162 time to fit residues: 113.6531 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 143 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1483 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 = 0.4088 r_free = 0.4088 target = 0.180133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154932 restraints weight = 16040.553| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.65 r_work: 0.3741 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13667 Z= 0.104 Angle : 0.502 7.812 18717 Z= 0.267 Chirality : 0.040 0.305 2010 Planarity : 0.004 0.059 2203 Dihedral : 15.892 113.666 2551 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 15.08 % Favored : 82.50 % 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: 0.47 (0.22), residues: 1453 helix: 1.39 (0.28), residues: 353 sheet: 0.15 (0.27), residues: 318 loop : -0.03 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 896 TYR 0.009 0.001 TYR A 958 PHE 0.013 0.001 PHE A 757 TRP 0.009 0.001 TRP A1549 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00230 (13651) covalent geometry : angle 0.49966 (18696) hydrogen bonds : bond 0.03264 ( 470) hydrogen bonds : angle 4.68526 ( 1316) metal coordination : bond 0.00398 ( 16) metal coordination : angle 1.66478 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.393 Fit side-chains REVERT: A 28 LYS cc_start: 0.6741 (ttmt) cc_final: 0.6383 (ttpt) REVERT: A 158 LYS cc_start: 0.7845 (mptm) cc_final: 0.6025 (ptpp) REVERT: A 165 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7856 (mttp) REVERT: A 179 LYS cc_start: 0.7890 (tptm) cc_final: 0.7314 (mttp) REVERT: A 209 LYS cc_start: 0.7986 (mttp) cc_final: 0.7458 (mtmm) REVERT: A 213 GLU cc_start: 0.7960 (mp0) cc_final: 0.7581 (mp0) REVERT: A 423 GLU cc_start: 0.7331 (pt0) cc_final: 0.6566 (pm20) REVERT: A 577 TYR cc_start: 0.7602 (p90) cc_final: 0.7322 (p90) REVERT: A 651 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7052 (ptt180) REVERT: A 692 MET cc_start: 0.5985 (ptm) cc_final: 0.5022 (pmt) REVERT: A 798 ASP cc_start: 0.7662 (m-30) cc_final: 0.7355 (m-30) REVERT: A 849 LYS cc_start: 0.6895 (tptp) cc_final: 0.6569 (tmtt) REVERT: A 894 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7079 (mmtt) REVERT: A 932 LYS cc_start: 0.6985 (mttm) cc_final: 0.6562 (mtmt) REVERT: A 1000 LYS cc_start: 0.7620 (mptt) cc_final: 0.6938 (tmmm) REVERT: A 1041 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7016 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5660 (pp20) REVERT: A 1131 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: A 1132 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6410 (pm20) outliers start: 31 outliers final: 18 residues processed: 147 average time/residue: 0.7425 time to fit residues: 117.3283 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153145 restraints weight = 16182.667| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.67 r_work: 0.3720 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13667 Z= 0.130 Angle : 0.529 9.201 18717 Z= 0.282 Chirality : 0.041 0.317 2010 Planarity : 0.004 0.059 2203 Dihedral : 15.868 113.132 2550 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.19 % Allowed : 15.62 % Favored : 82.19 % 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: 0.39 (0.22), residues: 1453 helix: 1.31 (0.28), residues: 352 sheet: 0.11 (0.27), residues: 323 loop : -0.08 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1036 TYR 0.010 0.001 TYR A 492 PHE 0.016 0.001 PHE A 757 TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00291 (13651) covalent geometry : angle 0.52626 (18696) hydrogen bonds : bond 0.03543 ( 470) hydrogen bonds : angle 4.75289 ( 1316) metal coordination : bond 0.00380 ( 16) metal coordination : angle 1.78395 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.529 Fit side-chains REVERT: A 28 LYS cc_start: 0.6769 (ttmt) cc_final: 0.6402 (ttpt) REVERT: A 158 LYS cc_start: 0.7869 (mptm) cc_final: 0.6022 (ptpp) REVERT: A 165 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7895 (mttp) REVERT: A 179 LYS cc_start: 0.7913 (tptm) cc_final: 0.7324 (mttp) REVERT: A 209 LYS cc_start: 0.8024 (mttp) cc_final: 0.7500 (mtmm) REVERT: A 213 GLU cc_start: 0.7985 (mp0) cc_final: 0.7641 (mp0) REVERT: A 423 GLU cc_start: 0.7310 (pt0) cc_final: 0.6530 (pm20) REVERT: A 651 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7096 (ptt180) REVERT: A 692 MET cc_start: 0.5954 (ptm) cc_final: 0.5058 (pmt) REVERT: A 798 ASP cc_start: 0.7765 (m-30) cc_final: 0.7467 (m-30) REVERT: A 849 LYS cc_start: 0.6921 (tptp) cc_final: 0.6591 (tmtt) REVERT: A 894 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7109 (mmtt) REVERT: A 896 ARG cc_start: 0.6874 (ttp80) cc_final: 0.6280 (ptm160) REVERT: A 932 LYS cc_start: 0.7094 (mttm) cc_final: 0.6693 (mtmt) REVERT: A 980 ASP cc_start: 0.8138 (p0) cc_final: 0.7869 (p0) REVERT: A 1000 LYS cc_start: 0.7611 (mptt) cc_final: 0.6939 (tmmm) REVERT: A 1041 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7033 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5694 (pp20) REVERT: A 1131 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: A 1132 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6416 (pm20) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.7159 time to fit residues: 109.5478 Evaluate side-chains 145 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.178427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153005 restraints weight = 16100.996| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.66 r_work: 0.3720 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13667 Z= 0.131 Angle : 0.533 8.420 18717 Z= 0.283 Chirality : 0.041 0.319 2010 Planarity : 0.004 0.059 2203 Dihedral : 15.874 113.002 2550 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.19 % Allowed : 15.86 % Favored : 81.95 % 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: 0.36 (0.22), residues: 1453 helix: 1.29 (0.28), residues: 352 sheet: 0.10 (0.27), residues: 321 loop : -0.10 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 896 TYR 0.010 0.001 TYR A 958 PHE 0.016 0.001 PHE A 757 TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00293 (13651) covalent geometry : angle 0.52961 (18696) hydrogen bonds : bond 0.03554 ( 470) hydrogen bonds : angle 4.77565 ( 1316) metal coordination : bond 0.00340 ( 16) metal coordination : angle 1.81542 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.490 Fit side-chains REVERT: A 28 LYS cc_start: 0.6784 (ttmt) cc_final: 0.6420 (ttpt) REVERT: A 158 LYS cc_start: 0.7876 (mptm) cc_final: 0.6020 (ptpp) REVERT: A 165 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7891 (mttp) REVERT: A 179 LYS cc_start: 0.7902 (tptm) cc_final: 0.7326 (mttp) REVERT: A 209 LYS cc_start: 0.8048 (mttp) cc_final: 0.7520 (mtmm) REVERT: A 213 GLU cc_start: 0.7983 (mp0) cc_final: 0.7588 (mp0) REVERT: A 423 GLU cc_start: 0.7416 (pt0) cc_final: 0.6640 (pm20) REVERT: A 651 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7098 (ptt180) REVERT: A 692 MET cc_start: 0.5963 (ptm) cc_final: 0.5042 (pmt) REVERT: A 798 ASP cc_start: 0.7776 (m-30) cc_final: 0.7490 (m-30) REVERT: A 849 LYS cc_start: 0.6933 (tptp) cc_final: 0.6603 (tmtt) REVERT: A 894 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7094 (mmtt) REVERT: A 896 ARG cc_start: 0.6874 (ttp80) cc_final: 0.6221 (ptp-110) REVERT: A 932 LYS cc_start: 0.7132 (mttm) cc_final: 0.6751 (mtmt) REVERT: A 980 ASP cc_start: 0.8192 (p0) cc_final: 0.7910 (p0) REVERT: A 1000 LYS cc_start: 0.7616 (mptt) cc_final: 0.6937 (tmmm) REVERT: A 1041 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7044 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5678 (pp20) REVERT: A 1131 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 1132 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6410 (pm20) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.7191 time to fit residues: 110.1782 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1387 MET Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 114 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 109 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151929 restraints weight = 16033.390| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.66 r_work: 0.3707 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13667 Z= 0.148 Angle : 0.553 8.237 18717 Z= 0.294 Chirality : 0.042 0.328 2010 Planarity : 0.005 0.060 2203 Dihedral : 15.896 112.976 2550 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.03 % Allowed : 15.86 % Favored : 82.11 % 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: 0.30 (0.22), residues: 1453 helix: 1.19 (0.28), residues: 352 sheet: 0.10 (0.27), residues: 322 loop : -0.13 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1036 TYR 0.010 0.001 TYR A 958 PHE 0.018 0.002 PHE A 757 TRP 0.011 0.001 TRP A1600 HIS 0.004 0.001 HIS A 741 Details of bonding type rmsd covalent geometry : bond 0.00332 (13651) covalent geometry : angle 0.54982 (18696) hydrogen bonds : bond 0.03776 ( 470) hydrogen bonds : angle 4.84942 ( 1316) metal coordination : bond 0.00392 ( 16) metal coordination : angle 1.92990 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5335.13 seconds wall clock time: 91 minutes 22.64 seconds (5482.64 seconds total)