Starting phenix.real_space_refine on Fri Jul 3 10:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wah_32385/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_2026/7wah_32385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wah_32385/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.68, per 1000 atoms: 0.20 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: 1.00 Conformation dependent library (CDL) restraints added in 505.7 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: 2.42 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: 4.43 Time building geometry restraints manager: 1.26 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: 7818 23.25 - 46.51: 248 46.51 - 69.76: 39 69.76 - 93.01: 6 93.01 - 116.27: 2 Dihedral angle restraints: 8113 sinusoidal: 3872 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 8110 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: 12.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 17.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 11.560 116.269 5377 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/Z covalent geometry : bond 0.00229 / 0.12 (13651) covalent geometry : angle 0.50862 / 0.29 (18696) hydrogen bonds : bond 0.16084 / 9.23 ( 470) hydrogen bonds : angle 6.62964 / 3.91 ( 1316) metal coordination : bond 0.01017 / 0.54 ( 16) metal coordination : angle 1.57217 / 0.53 ( 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 : 0.463 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: 0.6320 time to fit residues: 169.4877 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 : 0.432 ------------------------------------------------------------------------------- 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... 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 = 0.180549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154843 restraints weight = 15953.349| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.66 r_work: 0.3736 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1296 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 6.669 18717 Z= 0.295 Chirality : 0.042 0.327 2010 Planarity : 0.005 0.066 2203 Dihedral : 10.947 114.099 2349 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.19 % Allowed : 10.86 % Favored : 86.95 % 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: 0.51 (0.22), residues: 1453 helix: 1.27 (0.28), residues: 349 sheet: 0.37 (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 0.015 0.002 PHE A 757 TRP 0.011 0.001 TRP A1600 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (13651) covalent geometry : angle 0.54730 / 0.29 (18696) hydrogen bonds : bond 0.04222 / 2.47 ( 470) hydrogen bonds : angle 5.23736 / 3.16 ( 1316) metal coordination : bond 0.00692 / 0.45 ( 16) metal coordination : angle 2.01880 / 0.68 ( 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 176 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.326 Fit side-chains REVERT: A 13 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 28 LYS cc_start: 0.6851 (ttmt) cc_final: 0.6542 (ttpt) REVERT: A 158 LYS cc_start: 0.7674 (mmtt) cc_final: 0.5981 (ptpp) REVERT: A 165 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7860 (mttp) REVERT: A 179 LYS cc_start: 0.7807 (tptm) cc_final: 0.7111 (mttp) REVERT: A 209 LYS cc_start: 0.7979 (mttp) cc_final: 0.7600 (mtmp) REVERT: A 213 GLU cc_start: 0.7888 (mp0) cc_final: 0.7444 (mp0) REVERT: A 423 GLU cc_start: 0.7412 (pt0) cc_final: 0.6928 (pm20) REVERT: A 584 ASP cc_start: 0.7884 (t0) cc_final: 0.7584 (t70) REVERT: A 692 MET cc_start: 0.5840 (ptm) cc_final: 0.4851 (ttm) REVERT: A 787 GLU cc_start: 0.7737 (pt0) cc_final: 0.6378 (mm-30) REVERT: A 798 ASP cc_start: 0.7806 (m-30) cc_final: 0.7511 (m-30) REVERT: A 849 LYS cc_start: 0.6984 (tptp) cc_final: 0.6668 (tmtt) REVERT: A 1000 LYS cc_start: 0.7623 (mptt) cc_final: 0.6980 (tmmm) REVERT: A 1041 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7066 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6823 (tt0) cc_final: 0.6167 (tm130) REVERT: A 1115 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5874 (pp20) REVERT: A 1132 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6609 (pm20) REVERT: A 1194 LYS cc_start: 0.7356 (mmmt) cc_final: 0.7063 (mmmt) REVERT: A 1300 MET cc_start: 0.7561 (mmt) cc_final: 0.7336 (mmt) REVERT: A 1522 TRP cc_start: 0.6488 (m-10) cc_final: 0.6178 (m-10) outliers start: 28 outliers final: 11 residues processed: 164 average time/residue: 0.5894 time to fit residues: 104.4749 Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1084 ASN ** 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 = 0.4093 r_free = 0.4093 target = 0.180642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155018 restraints weight = 16025.854| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.67 r_work: 0.3739 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13667 Z= 0.120 Angle : 0.519 6.392 18717 Z= 0.276 Chirality : 0.041 0.316 2010 Planarity : 0.004 0.064 2203 Dihedral : 10.883 114.050 2348 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.66 % Allowed : 11.80 % Favored : 85.55 % 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: 0.55 (0.22), residues: 1453 helix: 1.39 (0.28), residues: 351 sheet: 0.29 (0.27), residues: 325 loop : 0.02 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1036 TYR 0.011 0.001 TYR A 577 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/Z covalent geometry : bond 0.00265 / 0.12 (13651) covalent geometry : angle 0.51569 / 0.28 (18696) hydrogen bonds : bond 0.03740 / 2.19 ( 470) hydrogen bonds : angle 4.97339 / 3.02 ( 1316) metal coordination : bond 0.00662 / 0.44 ( 16) metal coordination : angle 1.72876 / 0.59 ( 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 167 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.422 Fit side-chains REVERT: A 13 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 28 LYS cc_start: 0.6851 (ttmt) cc_final: 0.6519 (ttpt) REVERT: A 158 LYS cc_start: 0.7712 (mmtt) cc_final: 0.5989 (ptpp) REVERT: A 165 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7906 (mttp) REVERT: A 179 LYS cc_start: 0.7855 (tptm) cc_final: 0.7284 (mttp) REVERT: A 209 LYS cc_start: 0.7930 (mttp) cc_final: 0.7511 (mtmp) REVERT: A 213 GLU cc_start: 0.7846 (mp0) cc_final: 0.7453 (mp0) REVERT: A 277 LYS cc_start: 0.7889 (mtpm) cc_final: 0.7424 (mptt) REVERT: A 423 GLU cc_start: 0.7367 (pt0) cc_final: 0.6563 (pm20) REVERT: A 584 ASP cc_start: 0.7883 (t0) cc_final: 0.7569 (t70) REVERT: A 651 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7083 (ptt180) REVERT: A 692 MET cc_start: 0.5824 (ptm) cc_final: 0.4823 (ttp) REVERT: A 787 GLU cc_start: 0.7732 (pt0) cc_final: 0.6357 (mm-30) REVERT: A 798 ASP cc_start: 0.7781 (m-30) cc_final: 0.7475 (m-30) REVERT: A 849 LYS cc_start: 0.6981 (tptp) cc_final: 0.6643 (tmtt) REVERT: A 894 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7035 (mmtt) REVERT: A 1000 LYS cc_start: 0.7609 (mptt) cc_final: 0.6925 (tmmm) REVERT: A 1041 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7037 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: A 1132 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6554 (pm20) REVERT: A 1194 LYS cc_start: 0.7383 (mmmt) cc_final: 0.7086 (mmmt) outliers start: 34 outliers final: 15 residues processed: 156 average time/residue: 0.6065 time to fit residues: 102.5981 Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 603 LEU 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 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 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 1444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8584 > 50: distance: 36 - 89: 29.681 distance: 39 - 86: 33.771 distance: 65 - 69: 27.510 distance: 69 - 70: 43.282 distance: 70 - 71: 4.572 distance: 70 - 73: 21.048 distance: 71 - 72: 6.195 distance: 71 - 78: 20.986 distance: 73 - 74: 23.445 distance: 75 - 76: 20.788 distance: 75 - 77: 44.091 distance: 79 - 80: 47.778 distance: 79 - 82: 52.887 distance: 80 - 81: 5.257 distance: 80 - 86: 41.384 distance: 82 - 83: 55.691 distance: 83 - 84: 14.430 distance: 86 - 87: 58.750 distance: 87 - 88: 19.678 distance: 87 - 90: 26.515 distance: 88 - 89: 11.172 distance: 88 - 94: 39.624 distance: 90 - 91: 41.409 distance: 91 - 92: 30.685 distance: 91 - 93: 15.292 distance: 94 - 95: 16.043 distance: 94 - 193: 32.201 distance: 95 - 96: 56.599 distance: 95 - 98: 10.253 distance: 96 - 97: 45.063 distance: 96 - 101: 36.358 distance: 97 - 190: 31.254 distance: 98 - 99: 25.586 distance: 98 - 100: 39.031 distance: 101 - 102: 7.614 distance: 102 - 103: 42.522 distance: 102 - 105: 27.375 distance: 103 - 104: 12.206 distance: 103 - 112: 12.365 distance: 105 - 106: 16.377 distance: 106 - 107: 26.119 distance: 106 - 108: 11.565 distance: 107 - 109: 9.206 distance: 108 - 110: 34.498 distance: 109 - 111: 10.857 distance: 110 - 111: 17.935 distance: 112 - 113: 22.979 distance: 113 - 114: 36.323 distance: 113 - 116: 28.732 distance: 114 - 115: 25.853 distance: 114 - 121: 19.665 distance: 116 - 117: 31.135 distance: 118 - 119: 11.277 distance: 118 - 120: 58.058 distance: 121 - 122: 26.816 distance: 122 - 123: 24.136 distance: 122 - 125: 20.531 distance: 123 - 124: 32.192 distance: 123 - 127: 14.676 distance: 125 - 126: 47.892 distance: 127 - 128: 29.247 distance: 128 - 129: 57.912 distance: 128 - 131: 41.894 distance: 129 - 130: 45.701 distance: 129 - 135: 59.854 distance: 131 - 132: 31.463 distance: 132 - 133: 18.437 distance: 132 - 134: 10.526 distance: 135 - 136: 41.661 distance: 135 - 141: 53.456 distance: 136 - 137: 11.625 distance: 136 - 139: 33.250 distance: 137 - 138: 18.721 distance: 137 - 142: 13.504 distance: 139 - 140: 14.658 distance: 140 - 141: 44.211 distance: 142 - 143: 14.990 distance: 143 - 144: 10.868 distance: 143 - 146: 40.238 distance: 144 - 145: 21.856 distance: 144 - 151: 35.153 distance: 146 - 147: 27.356 distance: 147 - 148: 19.401 distance: 148 - 149: 3.194 distance: 148 - 150: 36.032