Starting phenix.real_space_refine on Fri Jun 28 19:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9f_27260/06_2024/8d9f_27260.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 33 5.49 5 S 57 5.16 5 C 10177 2.51 5 N 2793 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B GLU 765": "OE1" <-> "OE2" Residue "B GLU 939": "OE1" <-> "OE2" Residue "B ARG 1441": "NH1" <-> "NH2" Residue "B GLU 1455": "OE1" <-> "OE2" Residue "B ARG 1458": "NH1" <-> "NH2" Residue "B GLU 1505": "OE1" <-> "OE2" Residue "B ARG 1518": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5436 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1242, 10034 Classifications: {'peptide': 1242} Link IDs: {'PTRANS': 59, 'TRANS': 1182} Chain breaks: 7 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 2, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 13} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6104 SG CYS B 83 38.936 26.446 26.156 1.00133.42 S ATOM 6375 SG CYS B 116 36.827 23.888 24.100 1.00155.67 S ATOM 6421 SG CYS B 122 37.693 23.283 27.769 1.00130.57 S ATOM 6445 SG CYS B 125 35.328 26.034 26.846 1.00125.50 S ATOM 9139 SG CYS B 486 50.070 47.433 49.719 1.00127.38 S ATOM 9207 SG CYS B 496 48.620 45.167 46.905 1.00118.87 S ATOM 9221 SG CYS B 498 52.348 45.172 48.258 1.00121.83 S ATOM 9243 SG CYS B 501 49.427 43.592 50.006 1.00119.03 S ATOM 11214 SG CYS B 745 54.251 67.386 72.428 1.00150.38 S ATOM 11227 SG CYS B 747 56.315 65.418 74.936 1.00140.80 S ATOM 11249 SG CYS B 750 53.200 63.747 73.492 1.00136.31 S ATOM 13200 SG CYS B1013 46.791 71.941 109.540 1.00179.40 S ATOM 13326 SG CYS B1401 46.249 73.597 106.140 1.00176.13 S ATOM 13377 SG CYS B1409 49.714 73.209 107.752 1.00162.63 S ATOM 13394 SG CYS B1412 48.089 70.245 106.283 1.00153.82 S Time building chain proxies: 9.14, per 1000 atoms: 0.57 Number of scatterers: 16163 At special positions: 0 Unit cell: (102.72, 104.86, 156.22, 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 57 16.00 P 33 15.00 O 3099 8.00 N 2793 7.00 C 10177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.00 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 125 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 122 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 83 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 116 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 496 " pdb=" ZN B1703 " pdb="ZN ZN B1703 " - pdb=" ND1 HIS B 742 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 747 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 745 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 750 " pdb=" ZN B1704 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1409 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1013 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1412 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1401 " Number of angles added : 21 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 25 sheets defined 42.0% alpha, 18.0% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.658A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.572A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.772A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.372A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 230 through 246 removed outlier: 4.083A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 279 through 297 removed outlier: 4.737A pdb=" N VAL A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.587A pdb=" N LYS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 362 removed outlier: 4.023A pdb=" N TYR A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.967A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.720A pdb=" N ALA A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.558A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 3.763A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.579A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 54 through 73 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.532A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 302 removed outlier: 3.694A pdb=" N ILE B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 681 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.664A pdb=" N LYS B 799 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 843 Processing helix chain 'B' and resid 868 through 878 removed outlier: 4.020A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1010 removed outlier: 3.613A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1458 through 1463 removed outlier: 4.355A pdb=" N SER B1462 " --> pdb=" O ARG B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.548A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 removed outlier: 3.598A pdb=" N VAL B1496 " --> pdb=" O ILE B1492 " (cutoff:3.500A) Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1578 through 1597 Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.573A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275 Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.368A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 622 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR A 660 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 624 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 587 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.133A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.189A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.528A pdb=" N THR B 4 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 8 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.528A pdb=" N VAL B 80 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.136A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 426 through 427 removed outlier: 3.535A pdb=" N VAL B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 525 Processing sheet with id=AB6, first strand: chain 'B' and resid 528 through 529 removed outlier: 3.679A pdb=" N THR B 534 " --> pdb=" O ASN B 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 694 through 695 removed outlier: 7.201A pdb=" N ALA B 694 " --> pdb=" O TYR B 803 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC2, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC3, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC4, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.051A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1416 through 1417 Processing sheet with id=AC7, first strand: chain 'B' and resid 1448 through 1450 691 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2654 1.32 - 1.44: 4650 1.44 - 1.56: 9169 1.56 - 1.69: 35 1.69 - 1.81: 80 Bond restraints: 16588 Sorted by residual: bond pdb=" O3' A C 28 " pdb=" P C C 29 " ideal model delta sigma weight residual 1.607 1.459 0.148 1.50e-02 4.44e+03 9.71e+01 bond pdb=" O3' U C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 1.607 1.460 0.147 1.50e-02 4.44e+03 9.64e+01 bond pdb=" O3' G C 20 " pdb=" P U C 21 " ideal model delta sigma weight residual 1.607 1.477 0.130 1.50e-02 4.44e+03 7.48e+01 bond pdb=" O3' U C 36 " pdb=" P U C 37 " ideal model delta sigma weight residual 1.607 1.490 0.117 1.50e-02 4.44e+03 6.05e+01 bond pdb=" O3' U C 27 " pdb=" P A C 28 " ideal model delta sigma weight residual 1.607 1.492 0.115 1.50e-02 4.44e+03 5.91e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 80.49 - 91.20: 2 91.20 - 101.91: 114 101.91 - 112.61: 9150 112.61 - 123.32: 12514 123.32 - 134.03: 731 Bond angle restraints: 22511 Sorted by residual: angle pdb=" O2' U C 16 " pdb=" C2' U C 16 " pdb=" C1' U C 16 " ideal model delta sigma weight residual 108.40 80.49 27.91 1.50e+00 4.44e-01 3.46e+02 angle pdb=" O2' U C 35 " pdb=" C2' U C 35 " pdb=" C1' U C 35 " ideal model delta sigma weight residual 108.40 88.18 20.22 1.50e+00 4.44e-01 1.82e+02 angle pdb=" O2' A C 32 " pdb=" C2' A C 32 " pdb=" C1' A C 32 " ideal model delta sigma weight residual 111.80 96.72 15.08 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O2' C C 30 " pdb=" C2' C C 30 " pdb=" C1' C C 30 " ideal model delta sigma weight residual 108.40 93.49 14.91 1.50e+00 4.44e-01 9.89e+01 angle pdb=" C4' C C 43 " pdb=" C3' C C 43 " pdb=" O3' C C 43 " ideal model delta sigma weight residual 109.40 94.49 14.91 1.50e+00 4.44e-01 9.88e+01 ... (remaining 22506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 9773 34.95 - 69.90: 210 69.90 - 104.85: 28 104.85 - 139.81: 1 139.81 - 174.76: 7 Dihedral angle restraints: 10019 sinusoidal: 4509 harmonic: 5510 Sorted by residual: dihedral pdb=" O4' C C 31 " pdb=" C1' C C 31 " pdb=" N1 C C 31 " pdb=" C2 C C 31 " ideal model delta sinusoidal sigma weight residual 200.00 34.07 165.93 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' C C 30 " pdb=" C1' C C 30 " pdb=" N1 C C 30 " pdb=" C2 C C 30 " ideal model delta sinusoidal sigma weight residual 200.00 37.21 162.79 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' C C 14 " pdb=" C1' C C 14 " pdb=" N1 C C 14 " pdb=" C2 C C 14 " ideal model delta sinusoidal sigma weight residual 200.00 38.90 161.10 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 10016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2370 0.154 - 0.308: 51 0.308 - 0.463: 8 0.463 - 0.617: 2 0.617 - 0.771: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" P G C 12 " pdb=" OP1 G C 12 " pdb=" OP2 G C 12 " pdb=" O5' G C 12 " both_signs ideal model delta sigma weight residual True 2.41 -1.64 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" P G C 20 " pdb=" OP1 G C 20 " pdb=" OP2 G C 20 " pdb=" O5' G C 20 " both_signs ideal model delta sigma weight residual True 2.41 -1.85 0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" C3' A C 23 " pdb=" C4' A C 23 " pdb=" O3' A C 23 " pdb=" C2' A C 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2429 not shown) Planarity restraints: 2774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.102 2.00e-02 2.50e+03 4.58e-02 5.77e+01 pdb=" N9 A C 28 " -0.100 2.00e-02 2.50e+03 pdb=" C8 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A C 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.021 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.031 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.023 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.022 2.00e-02 2.50e+03 pdb=" C4 A C 28 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 18 " -0.036 2.00e-02 2.50e+03 2.79e-02 2.13e+01 pdb=" N9 A C 18 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A C 18 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A C 18 " 0.033 2.00e-02 2.50e+03 pdb=" C5 A C 18 " 0.037 2.00e-02 2.50e+03 pdb=" C6 A C 18 " -0.023 2.00e-02 2.50e+03 pdb=" N6 A C 18 " -0.032 2.00e-02 2.50e+03 pdb=" N1 A C 18 " -0.016 2.00e-02 2.50e+03 pdb=" C2 A C 18 " 0.012 2.00e-02 2.50e+03 pdb=" N3 A C 18 " 0.031 2.00e-02 2.50e+03 pdb=" C4 A C 18 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1497 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B1498 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B1498 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B1498 " 0.061 5.00e-02 4.00e+02 ... (remaining 2771 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 14332 3.17 - 3.75: 25318 3.75 - 4.32: 36539 4.32 - 4.90: 60032 Nonbonded interactions: 136385 Sorted by model distance: nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.015 2.440 nonbonded pdb=" OG SER B 849 " pdb=" OP2 U C 35 " model vdw 2.059 2.440 nonbonded pdb=" O ILE B1594 " pdb=" OG SER B1597 " model vdw 2.172 2.440 nonbonded pdb=" O GLN B 904 " pdb=" NZ LYS B1622 " model vdw 2.172 2.520 nonbonded pdb=" CE1 PHE A 542 " pdb=" CE1 HIS A 585 " model vdw 2.195 3.560 ... (remaining 136380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.630 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: 3.130 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 51.340 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.010 0.148 16588 Z= 0.624 Angle : 0.943 27.911 22511 Z= 0.568 Chirality : 0.063 0.771 2432 Planarity : 0.005 0.113 2774 Dihedral : 15.696 174.757 6475 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1890 helix: 1.23 (0.19), residues: 731 sheet: 0.03 (0.31), residues: 263 loop : -0.23 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1625 HIS 0.006 0.001 HIS A 585 PHE 0.027 0.002 PHE B 825 TYR 0.029 0.002 TYR B 524 ARG 0.011 0.001 ARG B1583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8756 (m-30) cc_final: 0.8331 (m-30) REVERT: A 138 GLU cc_start: 0.9294 (tp30) cc_final: 0.8941 (tm-30) REVERT: A 139 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9183 (mmmm) REVERT: A 180 MET cc_start: 0.9260 (mmm) cc_final: 0.9049 (mmm) REVERT: A 287 MET cc_start: 0.8990 (mtm) cc_final: 0.8772 (mtm) REVERT: A 682 TYR cc_start: 0.8509 (m-10) cc_final: 0.8206 (m-10) REVERT: B 273 GLU cc_start: 0.9138 (tp30) cc_final: 0.8819 (mm-30) REVERT: B 283 ASP cc_start: 0.9232 (t70) cc_final: 0.9006 (t0) REVERT: B 310 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8541 (mm-30) REVERT: B 672 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 876 ASN cc_start: 0.9236 (m110) cc_final: 0.8897 (m-40) REVERT: B 956 LEU cc_start: 0.9014 (mm) cc_final: 0.8771 (mm) REVERT: B 1581 ASP cc_start: 0.9253 (m-30) cc_final: 0.8957 (m-30) REVERT: B 1583 ARG cc_start: 0.8950 (ptp90) cc_final: 0.8647 (mtm-85) REVERT: B 1590 TYR cc_start: 0.9256 (t80) cc_final: 0.8933 (t80) REVERT: B 1621 TYR cc_start: 0.8304 (m-80) cc_final: 0.8023 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 1.4323 time to fit residues: 304.6247 Evaluate side-chains 144 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1507 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 152 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 147 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16588 Z= 0.173 Angle : 0.559 8.501 22511 Z= 0.291 Chirality : 0.040 0.221 2432 Planarity : 0.004 0.068 2774 Dihedral : 14.818 178.713 2581 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.71 % Allowed : 7.56 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1890 helix: 1.91 (0.20), residues: 726 sheet: 0.36 (0.31), residues: 265 loop : -0.09 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1437 HIS 0.006 0.001 HIS A 585 PHE 0.018 0.001 PHE A 491 TYR 0.025 0.001 TYR B1585 ARG 0.010 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8086 (tp30) REVERT: A 117 ASP cc_start: 0.8731 (m-30) cc_final: 0.8341 (m-30) REVERT: A 138 GLU cc_start: 0.9240 (tp30) cc_final: 0.8879 (tm-30) REVERT: A 139 LYS cc_start: 0.9530 (mmpt) cc_final: 0.9163 (mmmm) REVERT: A 180 MET cc_start: 0.9194 (mmm) cc_final: 0.8973 (mmm) REVERT: A 467 GLU cc_start: 0.8736 (pp20) cc_final: 0.8185 (pp20) REVERT: A 504 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8633 (pptt) REVERT: A 682 TYR cc_start: 0.8578 (m-10) cc_final: 0.8189 (m-10) REVERT: B 31 MET cc_start: 0.8944 (tpp) cc_final: 0.8336 (tpp) REVERT: B 273 GLU cc_start: 0.9110 (tp30) cc_final: 0.8813 (mm-30) REVERT: B 277 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 283 ASP cc_start: 0.9212 (t70) cc_final: 0.8964 (t0) REVERT: B 384 TYR cc_start: 0.8913 (t80) cc_final: 0.8712 (t80) REVERT: B 672 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 693 ASP cc_start: 0.8490 (m-30) cc_final: 0.8125 (m-30) REVERT: B 876 ASN cc_start: 0.9251 (m110) cc_final: 0.8895 (m-40) REVERT: B 942 GLU cc_start: 0.8356 (tp30) cc_final: 0.8084 (tp30) REVERT: B 956 LEU cc_start: 0.9033 (mm) cc_final: 0.8829 (mm) REVERT: B 980 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8493 (mtmt) REVERT: B 1581 ASP cc_start: 0.9205 (m-30) cc_final: 0.8841 (m-30) REVERT: B 1583 ARG cc_start: 0.8926 (ptp90) cc_final: 0.8698 (ptt90) REVERT: B 1590 TYR cc_start: 0.9210 (t80) cc_final: 0.8946 (t80) outliers start: 12 outliers final: 3 residues processed: 182 average time/residue: 1.3106 time to fit residues: 264.0341 Evaluate side-chains 146 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1677 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 176 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS B 323 HIS B 876 ASN ** B 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 16588 Z= 0.443 Angle : 0.608 8.087 22511 Z= 0.317 Chirality : 0.043 0.212 2432 Planarity : 0.004 0.058 2774 Dihedral : 14.708 178.121 2578 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.67 % Allowed : 9.29 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1890 helix: 1.86 (0.19), residues: 729 sheet: 0.46 (0.31), residues: 261 loop : -0.16 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1596 HIS 0.004 0.001 HIS A 457 PHE 0.020 0.001 PHE A 491 TYR 0.021 0.002 TYR B1640 ARG 0.007 0.001 ARG B1639 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8124 (tp30) REVERT: A 117 ASP cc_start: 0.8780 (m-30) cc_final: 0.8394 (m-30) REVERT: A 138 GLU cc_start: 0.9268 (tp30) cc_final: 0.8892 (tm-30) REVERT: A 139 LYS cc_start: 0.9534 (mmpt) cc_final: 0.9221 (mmmm) REVERT: A 180 MET cc_start: 0.9339 (mmm) cc_final: 0.9091 (mmm) REVERT: A 504 LYS cc_start: 0.8829 (ptmm) cc_final: 0.8595 (pptt) REVERT: A 682 TYR cc_start: 0.8599 (m-10) cc_final: 0.8391 (m-10) REVERT: B 31 MET cc_start: 0.8980 (tpp) cc_final: 0.8440 (tpp) REVERT: B 273 GLU cc_start: 0.9188 (tp30) cc_final: 0.8895 (mm-30) REVERT: B 283 ASP cc_start: 0.9250 (t70) cc_final: 0.8980 (t0) REVERT: B 672 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 876 ASN cc_start: 0.9313 (m-40) cc_final: 0.8926 (m110) REVERT: B 938 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: B 942 GLU cc_start: 0.8390 (tp30) cc_final: 0.8131 (tp30) REVERT: B 1447 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7601 (ttp80) REVERT: B 1581 ASP cc_start: 0.9213 (m-30) cc_final: 0.8857 (m-30) REVERT: B 1583 ARG cc_start: 0.8956 (ptp90) cc_final: 0.8739 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9247 (t80) cc_final: 0.8962 (t80) REVERT: B 1639 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7437 (mtm110) outliers start: 28 outliers final: 4 residues processed: 162 average time/residue: 1.3553 time to fit residues: 243.6001 Evaluate side-chains 137 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1624 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1532 GLN ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16588 Z= 0.189 Angle : 0.530 7.651 22511 Z= 0.274 Chirality : 0.039 0.211 2432 Planarity : 0.004 0.051 2774 Dihedral : 14.599 178.401 2578 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.61 % Allowed : 10.36 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1890 helix: 2.08 (0.19), residues: 729 sheet: 0.51 (0.31), residues: 263 loop : -0.10 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1596 HIS 0.005 0.001 HIS B1616 PHE 0.017 0.001 PHE A 491 TYR 0.022 0.001 TYR B1640 ARG 0.005 0.000 ARG B1639 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7987 (tp30) REVERT: A 117 ASP cc_start: 0.8832 (m-30) cc_final: 0.8433 (m-30) REVERT: A 138 GLU cc_start: 0.9246 (tp30) cc_final: 0.8918 (tm-30) REVERT: A 139 LYS cc_start: 0.9575 (mmpt) cc_final: 0.9236 (mmmm) REVERT: A 180 MET cc_start: 0.9162 (mmm) cc_final: 0.8838 (mmm) REVERT: A 235 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: A 504 LYS cc_start: 0.8785 (ptmm) cc_final: 0.8551 (pptt) REVERT: A 682 TYR cc_start: 0.8755 (m-10) cc_final: 0.8531 (m-10) REVERT: A 690 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 31 MET cc_start: 0.8892 (tpp) cc_final: 0.8537 (tpp) REVERT: B 273 GLU cc_start: 0.9130 (tp30) cc_final: 0.8796 (mm-30) REVERT: B 277 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 283 ASP cc_start: 0.9229 (t70) cc_final: 0.8929 (t0) REVERT: B 310 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8172 (mm-30) REVERT: B 384 TYR cc_start: 0.8893 (t80) cc_final: 0.8684 (t80) REVERT: B 583 MET cc_start: 0.8789 (tpp) cc_final: 0.8553 (mmm) REVERT: B 672 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 876 ASN cc_start: 0.9312 (m-40) cc_final: 0.8893 (m-40) REVERT: B 938 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: B 942 GLU cc_start: 0.8377 (tp30) cc_final: 0.8089 (tp30) REVERT: B 1488 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7832 (pttm) REVERT: B 1507 MET cc_start: 0.9111 (mmm) cc_final: 0.8554 (tpt) REVERT: B 1560 ASP cc_start: 0.9119 (t0) cc_final: 0.8876 (m-30) REVERT: B 1581 ASP cc_start: 0.9262 (m-30) cc_final: 0.8871 (m-30) REVERT: B 1583 ARG cc_start: 0.8937 (ptp90) cc_final: 0.8702 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9184 (t80) cc_final: 0.8894 (t80) REVERT: B 1639 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7326 (mtm110) outliers start: 27 outliers final: 8 residues processed: 179 average time/residue: 1.3122 time to fit residues: 260.4863 Evaluate side-chains 151 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1657 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16588 Z= 0.351 Angle : 0.574 9.105 22511 Z= 0.297 Chirality : 0.041 0.199 2432 Planarity : 0.004 0.047 2774 Dihedral : 14.526 179.192 2578 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.55 % Allowed : 12.50 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1890 helix: 1.99 (0.19), residues: 730 sheet: 0.49 (0.32), residues: 251 loop : -0.16 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.017 0.001 PHE A 491 TYR 0.016 0.001 TYR B1640 ARG 0.006 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8131 (tp30) REVERT: A 102 GLU cc_start: 0.8775 (tp30) cc_final: 0.7997 (tp30) REVERT: A 117 ASP cc_start: 0.8801 (m-30) cc_final: 0.8413 (m-30) REVERT: A 138 GLU cc_start: 0.9272 (tp30) cc_final: 0.8946 (tm-30) REVERT: A 139 LYS cc_start: 0.9541 (mmpt) cc_final: 0.9196 (mmmm) REVERT: A 180 MET cc_start: 0.9297 (mmm) cc_final: 0.8974 (mmm) REVERT: A 235 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: A 504 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8524 (pptt) REVERT: A 512 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8535 (mt-10) REVERT: A 690 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 31 MET cc_start: 0.8925 (tpp) cc_final: 0.8697 (tpp) REVERT: B 273 GLU cc_start: 0.9148 (tp30) cc_final: 0.8827 (mm-30) REVERT: B 277 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 283 ASP cc_start: 0.9257 (t70) cc_final: 0.8945 (t0) REVERT: B 310 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8086 (mm-30) REVERT: B 385 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 583 MET cc_start: 0.8796 (tpp) cc_final: 0.8463 (mmm) REVERT: B 672 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 876 ASN cc_start: 0.9331 (m-40) cc_final: 0.8919 (m-40) REVERT: B 938 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: B 942 GLU cc_start: 0.8407 (tp30) cc_final: 0.8097 (tp30) REVERT: B 1488 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7640 (pttp) REVERT: B 1560 ASP cc_start: 0.9154 (t0) cc_final: 0.8873 (m-30) REVERT: B 1581 ASP cc_start: 0.9264 (m-30) cc_final: 0.8874 (m-30) REVERT: B 1583 ARG cc_start: 0.8940 (ptp90) cc_final: 0.8706 (ptt90) REVERT: B 1590 TYR cc_start: 0.9171 (t80) cc_final: 0.8877 (t80) REVERT: B 1639 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7304 (mtm110) outliers start: 26 outliers final: 12 residues processed: 166 average time/residue: 1.3217 time to fit residues: 242.8460 Evaluate side-chains 157 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1522 LEU Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1657 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1404 > 50: distance: 10 - 97: 7.805 distance: 74 - 78: 13.833 distance: 78 - 79: 10.774 distance: 79 - 80: 11.005 distance: 79 - 82: 14.033 distance: 80 - 81: 23.523 distance: 80 - 87: 4.016 distance: 82 - 83: 13.372 distance: 83 - 84: 12.746 distance: 84 - 85: 7.180 distance: 84 - 86: 11.881 distance: 87 - 88: 10.262 distance: 87 - 93: 27.994 distance: 88 - 89: 13.780 distance: 88 - 91: 25.089 distance: 89 - 90: 17.691 distance: 89 - 94: 6.350 distance: 91 - 92: 20.654 distance: 92 - 93: 33.690 distance: 94 - 95: 16.855 distance: 95 - 96: 18.396 distance: 95 - 98: 16.752 distance: 96 - 97: 10.780 distance: 96 - 102: 19.309 distance: 98 - 99: 7.127 distance: 99 - 100: 14.065 distance: 99 - 101: 14.344 distance: 102 - 103: 19.650 distance: 104 - 105: 19.744 distance: 104 - 109: 22.747 distance: 106 - 107: 17.354 distance: 106 - 108: 20.763 distance: 109 - 110: 10.603 distance: 110 - 111: 27.149 distance: 110 - 113: 17.932 distance: 111 - 112: 41.783 distance: 111 - 120: 17.998 distance: 113 - 114: 9.775 distance: 114 - 115: 9.524 distance: 115 - 116: 6.050 distance: 116 - 117: 13.629 distance: 117 - 118: 7.896 distance: 117 - 119: 16.180 distance: 120 - 121: 29.247 distance: 121 - 122: 15.428 distance: 121 - 124: 45.591 distance: 122 - 123: 15.659 distance: 122 - 132: 33.887 distance: 124 - 125: 20.365 distance: 125 - 126: 7.409 distance: 125 - 127: 19.556 distance: 126 - 128: 13.490 distance: 127 - 129: 9.456 distance: 128 - 130: 5.994 distance: 129 - 130: 13.517 distance: 130 - 131: 13.140 distance: 132 - 133: 13.583 distance: 132 - 138: 4.731 distance: 133 - 134: 12.517 distance: 133 - 136: 15.974 distance: 134 - 135: 14.610 distance: 134 - 139: 25.609 distance: 136 - 137: 12.644 distance: 139 - 140: 4.576 distance: 140 - 141: 11.742 distance: 140 - 143: 6.675 distance: 141 - 142: 14.792 distance: 141 - 146: 15.514 distance: 143 - 144: 20.353 distance: 143 - 145: 15.873 distance: 146 - 147: 7.161 distance: 147 - 148: 7.767 distance: 147 - 150: 13.341 distance: 148 - 149: 12.576 distance: 150 - 151: 5.597 distance: 151 - 152: 26.803 distance: 151 - 153: 11.887 distance: 154 - 155: 8.534 distance: 155 - 156: 9.460 distance: 155 - 158: 6.148 distance: 156 - 157: 10.622 distance: 158 - 159: 11.373 distance: 159 - 160: 4.824 distance: 159 - 161: 4.019