Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:03:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/12_2022/7jmn_22397.pdb" } resolution = 3.58 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 ------------------------------------------------------------------------------- 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= 0.037 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ARG 85": "NH1" <-> "NH2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E GLU 641": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "E ARG 755": "NH1" <-> "NH2" Residue "E GLU 789": "OE1" <-> "OE2" Residue "E ASP 885": "OD1" <-> "OD2" Residue "N PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 850": "NH1" <-> "NH2" Residue "N ARG 852": "NH1" <-> "NH2" Residue "N ARG 880": "NH1" <-> "NH2" Residue "N GLU 911": "OE1" <-> "OE2" Residue "N GLU 919": "OE1" <-> "OE2" Residue "N ARG 938": "NH1" <-> "NH2" Residue "N ARG 946": "NH1" <-> "NH2" Residue "N GLU 956": "OE1" <-> "OE2" Residue "N ARG 967": "NH1" <-> "NH2" Residue "P ARG 72": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P ASP 178": "OD1" <-> "OD2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P GLU 283": "OE1" <-> "OE2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 421": "NH1" <-> "NH2" Residue "P ARG 492": "NH1" <-> "NH2" Residue "P GLU 503": "OE1" <-> "OE2" Residue "P GLU 522": "OE1" <-> "OE2" Residue "P TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 859": "NH1" <-> "NH2" Residue "P ARG 920": "NH1" <-> "NH2" Residue "P GLU 944": "OE1" <-> "OE2" Residue "O GLU 278": "OE1" <-> "OE2" Residue "O PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4467 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 34, 'TRANS': 549} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "N" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1439 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "P" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6178 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 49, 'TRANS': 760} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1290 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "X" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 259 Classifications: {'peptide': 52} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 51} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 8.16, per 1000 atoms: 0.60 Number of scatterers: 13633 At special positions: 0 Unit cell: (162.208, 164.4, 104.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2570 8.00 N 2391 7.00 C 8610 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: 5.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 37.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.714A pdb=" N TYR E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 230 removed outlier: 4.364A pdb=" N GLU E 225 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 removed outlier: 4.034A pdb=" N ILE E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS E 242 " --> pdb=" O CYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.880A pdb=" N LEU E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 391 removed outlier: 4.327A pdb=" N ILE E 383 " --> pdb=" O LYS E 379 " (cutoff:3.500A) Proline residue: E 387 - end of helix Processing helix chain 'E' and resid 397 through 405 removed outlier: 4.830A pdb=" N TYR E 402 " --> pdb=" O THR E 399 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.897A pdb=" N CYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.652A pdb=" N GLU E 481 " --> pdb=" O TYR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 515 through 524 removed outlier: 3.864A pdb=" N SER E 524 " --> pdb=" O ARG E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 528 Processing helix chain 'E' and resid 529 through 536 removed outlier: 3.960A pdb=" N LEU E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 535 " --> pdb=" O VAL E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.654A pdb=" N LYS E 540 " --> pdb=" O LYS E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 550 removed outlier: 3.697A pdb=" N GLU E 547 " --> pdb=" O HIS E 543 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU E 548 " --> pdb=" O PRO E 544 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU E 549 " --> pdb=" O LEU E 545 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 550 " --> pdb=" O CYS E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 583 removed outlier: 3.814A pdb=" N GLU E 567 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 572 " --> pdb=" O GLU E 568 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU E 576 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR E 583 " --> pdb=" O PHE E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 613 Proline residue: E 611 - end of helix Processing helix chain 'E' and resid 655 through 668 removed outlier: 3.650A pdb=" N ALA E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 681 Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 691 through 699 removed outlier: 3.750A pdb=" N ALA E 695 " --> pdb=" O ALA E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 718 Processing helix chain 'E' and resid 718 through 723 removed outlier: 3.758A pdb=" N LEU E 722 " --> pdb=" O LEU E 718 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 718 through 723' Processing helix chain 'E' and resid 728 through 757 removed outlier: 4.230A pdb=" N ASN E 740 " --> pdb=" O SER E 736 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL E 742 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS E 744 " --> pdb=" O ASN E 740 " (cutoff:3.500A) Proline residue: E 745 - end of helix removed outlier: 4.070A pdb=" N HIS E 748 " --> pdb=" O LYS E 744 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA E 749 " --> pdb=" O PRO E 745 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 750 " --> pdb=" O LEU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 769 removed outlier: 3.628A pdb=" N LEU E 767 " --> pdb=" O ILE E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 843 through 851 removed outlier: 4.241A pdb=" N GLN E 849 " --> pdb=" O LEU E 845 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 850 " --> pdb=" O ALA E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 867 removed outlier: 3.611A pdb=" N SER E 866 " --> pdb=" O ASP E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 882 Processing helix chain 'N' and resid 800 through 813 removed outlier: 4.156A pdb=" N GLN N 805 " --> pdb=" O ILE N 801 " (cutoff:3.500A) Processing helix chain 'N' and resid 814 through 819 removed outlier: 3.941A pdb=" N ARG N 818 " --> pdb=" O GLU N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 876 through 880 removed outlier: 3.677A pdb=" N ARG N 880 " --> pdb=" O VAL N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 882 through 889 removed outlier: 3.971A pdb=" N ASN N 886 " --> pdb=" O GLU N 882 " (cutoff:3.500A) Processing helix chain 'N' and resid 896 through 914 Proline residue: N 902 - end of helix Processing helix chain 'N' and resid 914 through 920 removed outlier: 3.861A pdb=" N GLN N 918 " --> pdb=" O TRP N 914 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU N 919 " --> pdb=" O GLN N 915 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN N 920 " --> pdb=" O THR N 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 914 through 920' Processing helix chain 'N' and resid 978 through 983 Processing helix chain 'N' and resid 995 through 1012 removed outlier: 4.369A pdb=" N GLY N 999 " --> pdb=" O SER N 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N1006 " --> pdb=" O THR N1002 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N1007 " --> pdb=" O GLY N1003 " (cutoff:3.500A) Proline residue: N1008 - end of helix Processing helix chain 'P' and resid 210 through 213 removed outlier: 4.118A pdb=" N VAL P 213 " --> pdb=" O HIS P 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 210 through 213' Processing helix chain 'P' and resid 563 through 568 removed outlier: 4.096A pdb=" N LYS P 566 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU P 567 " --> pdb=" O GLY P 564 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS P 568 " --> pdb=" O PRO P 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 563 through 568' Processing helix chain 'P' and resid 569 through 575 removed outlier: 3.907A pdb=" N SER P 573 " --> pdb=" O ALA P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 607 through 615 removed outlier: 3.884A pdb=" N THR P 611 " --> pdb=" O LYS P 607 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA P 612 " --> pdb=" O ASP P 608 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 641 Processing helix chain 'P' and resid 654 through 672 removed outlier: 3.920A pdb=" N GLN P 659 " --> pdb=" O ASN P 655 " (cutoff:3.500A) Proline residue: P 660 - end of helix removed outlier: 4.281A pdb=" N LYS P 666 " --> pdb=" O THR P 662 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN P 669 " --> pdb=" O GLY P 665 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU P 670 " --> pdb=" O LYS P 666 " (cutoff:3.500A) Processing helix chain 'P' and resid 699 through 726 removed outlier: 3.642A pdb=" N VAL P 703 " --> pdb=" O ASP P 699 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL P 704 " --> pdb=" O GLU P 700 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP P 705 " --> pdb=" O PRO P 701 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA P 706 " --> pdb=" O GLU P 702 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP P 713 " --> pdb=" O SER P 709 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU P 726 " --> pdb=" O THR P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 742 through 751 removed outlier: 3.970A pdb=" N TYR P 750 " --> pdb=" O ASP P 746 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 790 removed outlier: 3.885A pdb=" N GLY P 769 " --> pdb=" O SER P 765 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 773 " --> pdb=" O GLY P 769 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL P 780 " --> pdb=" O ARG P 776 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL P 781 " --> pdb=" O ARG P 777 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU P 782 " --> pdb=" O LEU P 778 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER P 783 " --> pdb=" O GLN P 779 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG P 787 " --> pdb=" O SER P 783 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA P 788 " --> pdb=" O LEU P 784 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 838 removed outlier: 4.107A pdb=" N ASP P 833 " --> pdb=" O ALA P 829 " (cutoff:3.500A) Processing helix chain 'P' and resid 850 through 868 removed outlier: 4.582A pdb=" N THR P 856 " --> pdb=" O SER P 852 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN P 857 " --> pdb=" O GLY P 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS P 861 " --> pdb=" O GLN P 857 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA P 862 " --> pdb=" O ILE P 858 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER P 863 " --> pdb=" O ARG P 859 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY P 866 " --> pdb=" O ALA P 862 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN P 868 " --> pdb=" O GLY P 864 " (cutoff:3.500A) Processing helix chain 'P' and resid 890 through 899 Processing helix chain 'P' and resid 923 through 927 removed outlier: 3.572A pdb=" N SER P 927 " --> pdb=" O ASP P 924 " (cutoff:3.500A) Processing helix chain 'P' and resid 937 through 942 removed outlier: 3.569A pdb=" N VAL P 940 " --> pdb=" O GLU P 937 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA P 941 " --> pdb=" O GLU P 938 " (cutoff:3.500A) Processing helix chain 'P' and resid 948 through 952 Processing helix chain 'O' and resid 89 through 104 removed outlier: 4.955A pdb=" N LEU O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 111 Processing helix chain 'O' and resid 134 through 147 Processing helix chain 'O' and resid 148 through 159 removed outlier: 3.845A pdb=" N GLN O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG O 159 " --> pdb=" O GLN O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 262 through 270 removed outlier: 4.377A pdb=" N GLN O 268 " --> pdb=" O ARG O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 284 removed outlier: 3.708A pdb=" N GLY O 283 " --> pdb=" O ASN O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 311 removed outlier: 4.162A pdb=" N GLN O 297 " --> pdb=" O ASN O 293 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE O 299 " --> pdb=" O VAL O 295 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR O 302 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET O 303 " --> pdb=" O PHE O 299 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU O 304 " --> pdb=" O ARG O 300 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU O 308 " --> pdb=" O LEU O 304 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS O 309 " --> pdb=" O GLN O 305 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'N' and resid 852 through 854 removed outlier: 4.247A pdb=" N LEU N 868 " --> pdb=" O ASP N 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 924 through 927 Processing sheet with id=AA3, first strand: chain 'N' and resid 962 through 963 Processing sheet with id=AA4, first strand: chain 'P' and resid 93 through 97 removed outlier: 3.699A pdb=" N VAL P 151 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 158 through 163 removed outlier: 3.574A pdb=" N GLU P 173 " --> pdb=" O PHE P 186 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE P 185 " --> pdb=" O SER P 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 215 through 217 Processing sheet with id=AA7, first strand: chain 'P' and resid 227 through 232 Processing sheet with id=AA8, first strand: chain 'P' and resid 299 through 305 removed outlier: 3.765A pdb=" N ILE P 299 " --> pdb=" O SER P 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA P 309 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 325 " --> pdb=" O ALA P 309 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL P 322 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY P 366 " --> pdb=" O VAL P 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 395 through 396 removed outlier: 3.769A pdb=" N ALA P 410 " --> pdb=" O LEU P 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 438 through 442 removed outlier: 3.562A pdb=" N LEU P 439 " --> pdb=" O GLN P 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 527 through 530 removed outlier: 3.719A pdb=" N GLN P 527 " --> pdb=" O VAL P 540 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE P 537 " --> pdb=" O VAL P 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 956 through 958 Processing sheet with id=AB4, first strand: chain 'X' and resid 66 through 68 368 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 5.66 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: 4601 1.34 - 1.46: 2675 1.46 - 1.58: 6517 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13885 Sorted by residual: bond pdb=" N ASP P 556 " pdb=" CA ASP P 556 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CA VAL E 606 " pdb=" CB VAL E 606 " ideal model delta sigma weight residual 1.551 1.532 0.018 1.08e-02 8.57e+03 2.91e+00 bond pdb=" CA GLY N 800 " pdb=" C GLY N 800 " ideal model delta sigma weight residual 1.513 1.527 -0.014 1.06e-02 8.90e+03 1.86e+00 bond pdb=" C THR O 272 " pdb=" N PRO O 273 " ideal model delta sigma weight residual 1.339 1.384 -0.044 3.40e-02 8.65e+02 1.71e+00 bond pdb=" C PHE P 916 " pdb=" N PRO P 917 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.56e+00 ... (remaining 13880 not shown) Histogram of bond angle deviations from ideal: 98.93 - 106.00: 366 106.00 - 113.07: 7578 113.07 - 120.14: 4986 120.14 - 127.22: 5802 127.22 - 134.29: 166 Bond angle restraints: 18898 Sorted by residual: angle pdb=" N PRO E 254 " pdb=" CA PRO E 254 " pdb=" CB PRO E 254 " ideal model delta sigma weight residual 103.25 111.61 -8.36 1.05e+00 9.07e-01 6.34e+01 angle pdb=" N PRO P 380 " pdb=" CA PRO P 380 " pdb=" CB PRO P 380 " ideal model delta sigma weight residual 103.25 111.18 -7.93 1.05e+00 9.07e-01 5.71e+01 angle pdb=" N PRO P 869 " pdb=" CA PRO P 869 " pdb=" CB PRO P 869 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.56e+01 angle pdb=" N PRO E 305 " pdb=" CA PRO E 305 " pdb=" CB PRO E 305 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 angle pdb=" N PRO O 188 " pdb=" CA PRO O 188 " pdb=" CB PRO O 188 " ideal model delta sigma weight residual 102.86 110.55 -7.69 1.23e+00 6.61e-01 3.91e+01 ... (remaining 18893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7457 17.48 - 34.96: 773 34.96 - 52.44: 125 52.44 - 69.93: 20 69.93 - 87.41: 12 Dihedral angle restraints: 8387 sinusoidal: 3141 harmonic: 5246 Sorted by residual: dihedral pdb=" CA GLY P 487 " pdb=" C GLY P 487 " pdb=" N THR P 488 " pdb=" CA THR P 488 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU E 472 " pdb=" C LEU E 472 " pdb=" N PRO E 473 " pdb=" CA PRO E 473 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PRO P 271 " pdb=" C PRO P 271 " pdb=" N GLN P 272 " pdb=" CA GLN P 272 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 8384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1727 0.055 - 0.110: 411 0.110 - 0.165: 54 0.165 - 0.220: 7 0.220 - 0.276: 4 Chirality restraints: 2203 Sorted by residual: chirality pdb=" CA PRO E 254 " pdb=" N PRO E 254 " pdb=" C PRO E 254 " pdb=" CB PRO E 254 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN P 899 " pdb=" N ASN P 899 " pdb=" C ASN P 899 " pdb=" CB ASN P 899 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO P 380 " pdb=" N PRO P 380 " pdb=" C PRO P 380 " pdb=" CB PRO P 380 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2200 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 791 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP E 791 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 791 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 791 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 791 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 791 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 791 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 95 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C LEU O 95 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU O 95 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN O 96 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 899 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO P 900 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO P 900 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO P 900 " 0.035 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 311 2.67 - 3.23: 13340 3.23 - 3.79: 17977 3.79 - 4.34: 23283 4.34 - 4.90: 38487 Nonbonded interactions: 93398 Sorted by model distance: nonbonded pdb=" OH TYR E 402 " pdb=" OG SER E 456 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASP E 530 " pdb=" OH TYR E 583 " model vdw 2.149 2.440 nonbonded pdb=" NE2 GLN P 413 " pdb=" OE1 GLN P 438 " model vdw 2.188 2.520 nonbonded pdb=" NZ LYS P 607 " pdb=" O GLN P 635 " model vdw 2.230 2.520 nonbonded pdb=" OE1 GLN O 268 " pdb=" OG SER O 282 " model vdw 2.237 2.440 ... (remaining 93393 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8610 2.51 5 N 2391 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 5.120 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: 23.130 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.120 Process input model: 35.440 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.004 0.053 13885 Z= 0.257 Angle : 0.828 13.987 18898 Z= 0.462 Chirality : 0.048 0.276 2203 Planarity : 0.005 0.062 2478 Dihedral : 14.636 87.407 4967 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.58 % Allowed : 19.25 % Favored : 80.16 % Rotamer Outliers : 0.07 % 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: -5.81 (0.16), residues: 1714 helix: -3.09 (0.16), residues: 616 sheet: -2.81 (0.35), residues: 175 loop : -4.85 (0.16), residues: 923 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.3032 time to fit residues: 93.8603 Evaluate side-chains 179 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1386 time to fit residues: 2.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5076 > 50: distance: 59 - 82: 37.030 distance: 75 - 82: 33.265 distance: 82 - 83: 13.004 distance: 83 - 84: 5.747 distance: 83 - 86: 16.098 distance: 84 - 85: 10.992 distance: 84 - 90: 15.977 distance: 86 - 87: 5.516 distance: 87 - 88: 8.074 distance: 90 - 91: 17.795 distance: 90 - 96: 19.299 distance: 91 - 92: 11.546 distance: 91 - 94: 25.745 distance: 92 - 93: 24.815 distance: 92 - 97: 14.570 distance: 94 - 95: 20.866 distance: 95 - 96: 22.458 distance: 97 - 98: 8.824 distance: 97 - 103: 28.323 distance: 98 - 99: 13.779 distance: 98 - 101: 22.517 distance: 99 - 100: 23.445 distance: 99 - 104: 11.366 distance: 101 - 102: 11.537 distance: 102 - 103: 14.303 distance: 104 - 105: 33.578 distance: 104 - 110: 31.132 distance: 105 - 106: 20.956 distance: 105 - 108: 11.302 distance: 106 - 107: 16.870 distance: 106 - 111: 9.940 distance: 108 - 109: 13.490 distance: 109 - 110: 6.144 distance: 111 - 112: 21.568 distance: 112 - 113: 11.020 distance: 113 - 114: 15.666 distance: 113 - 115: 7.380 distance: 115 - 116: 15.872 distance: 116 - 117: 6.865 distance: 116 - 119: 9.180 distance: 117 - 118: 16.764 distance: 117 - 126: 13.370 distance: 119 - 120: 7.082 distance: 120 - 121: 10.498 distance: 120 - 122: 20.951 distance: 121 - 123: 7.608 distance: 123 - 125: 13.541 distance: 124 - 125: 8.527 distance: 127 - 128: 8.090 distance: 127 - 130: 5.536 distance: 128 - 129: 15.162 distance: 128 - 137: 9.478 distance: 130 - 131: 10.070 distance: 131 - 132: 18.410 distance: 132 - 133: 4.824 distance: 133 - 134: 18.332 distance: 134 - 135: 7.605 distance: 134 - 136: 12.236 distance: 137 - 138: 7.190 distance: 138 - 139: 9.449 distance: 138 - 141: 7.871 distance: 139 - 140: 18.649 distance: 139 - 146: 12.806 distance: 141 - 142: 19.097 distance: 142 - 143: 16.999 distance: 143 - 144: 6.099 distance: 143 - 145: 19.476 distance: 146 - 147: 13.615 distance: 147 - 148: 11.829 distance: 147 - 150: 10.393 distance: 148 - 149: 10.320 distance: 148 - 153: 5.657 distance: 150 - 151: 17.310 distance: 150 - 152: 20.377 distance: 153 - 154: 23.507 distance: 154 - 155: 9.635 distance: 154 - 157: 20.961 distance: 155 - 156: 11.710 distance: 155 - 161: 17.088 distance: 157 - 158: 22.063 distance: 158 - 159: 10.924 distance: 158 - 160: 23.062