Starting phenix.real_space_refine on Sun Aug 4 03:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/08_2024/7xk0_33239.cif" } resolution = 3.59 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= 0.088 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: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 31 5.16 5 C 5581 2.51 5 N 1589 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 857": "OD1" <-> "OD2" Residue "A TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 897": "OD1" <-> "OD2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A ASP 1003": "OD1" <-> "OD2" Residue "A ASP 1010": "OD1" <-> "OD2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A ASP 1027": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Conformer: "B" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNA': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 9.50, per 1000 atoms: 1.03 Number of scatterers: 9208 At special positions: 0 Unit cell: (126.5, 106.7, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 73 15.00 O 1934 8.00 N 1589 7.00 C 5581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 43.9% alpha, 9.6% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.899A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.608A pdb=" N LEU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.629A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 256 through 273 removed outlier: 7.199A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.868A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 4.216A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.656A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.949A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.717A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.537A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.649A pdb=" N LYS A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.955A pdb=" N LEU A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.794A pdb=" N PHE A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 4.193A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 716 removed outlier: 3.727A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.065A pdb=" N ARG A 724 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 726 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER A 728 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.790A pdb=" N GLU A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 748 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.567A pdb=" N MET A 763 " --> pdb=" O ASN A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.793A pdb=" N LYS A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.589A pdb=" N THR A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.592A pdb=" N ARG A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 removed outlier: 3.594A pdb=" N ALA A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.760A pdb=" N ILE A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.809A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.696A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.811A pdb=" N VAL A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.666A pdb=" N SER A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 3.682A pdb=" N GLU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 removed outlier: 3.569A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 969' Processing helix chain 'A' and resid 990 through 1003 removed outlier: 4.417A pdb=" N SER A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.623A pdb=" N PHE A1014 " --> pdb=" O ASP A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1029 removed outlier: 3.595A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1055 removed outlier: 4.189A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 5.899A pdb=" N ALA A 91 " --> pdb=" O ALA A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 123 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'A' and resid 193 through 202 removed outlier: 6.427A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 216 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.907A pdb=" N ILE A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 427 removed outlier: 4.044A pdb=" N ASN A 440 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG A 384 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP A 542 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.575A pdb=" N LEU A 452 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 498 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR A 495 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG A 488 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 497 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 removed outlier: 7.198A pdb=" N PHE A 666 " --> pdb=" O CYS A 679 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS A 679 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 668 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 733 221 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1395 1.31 - 1.43: 2870 1.43 - 1.56: 5080 1.56 - 1.68: 145 1.68 - 1.81: 52 Bond restraints: 9542 Sorted by residual: bond pdb=" C8 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP B 1 " pdb=" PG GTP B 1 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.450 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.508 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.96: 655 106.96 - 114.51: 5693 114.51 - 122.06: 5214 122.06 - 129.61: 1637 129.61 - 137.16: 89 Bond angle restraints: 13288 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.92 -8.36 1.01e+00 9.80e-01 6.85e+01 angle pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " pdb=" C8 GTP B 1 " ideal model delta sigma weight residual 108.00 122.32 -14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 angle pdb=" C ARG A 529 " pdb=" N TRP A 530 " pdb=" CA TRP A 530 " ideal model delta sigma weight residual 122.58 113.93 8.65 2.07e+00 2.33e-01 1.75e+01 angle pdb=" N ILE A 945 " pdb=" CA ILE A 945 " pdb=" C ILE A 945 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 ... (remaining 13283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5550 35.70 - 71.39: 255 71.39 - 107.09: 32 107.09 - 142.78: 3 142.78 - 178.48: 2 Dihedral angle restraints: 5842 sinusoidal: 2984 harmonic: 2858 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 232.00 60.17 171.83 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O5' GTP B 1 " pdb=" O3A GTP B 1 " pdb=" PA GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 274.12 95.64 178.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual 260.87 139.34 121.54 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 5839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1162 0.060 - 0.120: 351 0.120 - 0.180: 46 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A 970 " pdb=" CA ILE A 970 " pdb=" CG1 ILE A 970 " pdb=" CG2 ILE A 970 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' U B 57 " pdb=" O4' U B 57 " pdb=" C2' U B 57 " pdb=" N1 U B 57 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 965 " pdb=" N ARG A 965 " pdb=" C ARG A 965 " pdb=" CB ARG A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1561 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ALA A 962 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 962 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 57 " -0.028 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" N1 U B 57 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 57 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 57 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U B 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 57 " 0.006 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1534 2.75 - 3.28: 8621 3.28 - 3.82: 14776 3.82 - 4.36: 17529 4.36 - 4.90: 28787 Nonbonded interactions: 71247 Sorted by model distance: nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.206 3.120 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 3.120 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.230 3.120 nonbonded pdb=" OE2 GLU A 233 " pdb=" OH TYR A 256 " model vdw 2.237 3.040 nonbonded pdb=" O PRO A 481 " pdb=" OG SER A 484 " model vdw 2.246 3.040 ... (remaining 71242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 36.250 Find NCS groups from input model: 0.100 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.011 0.173 9542 Z= 0.695 Angle : 0.958 14.317 13288 Z= 0.532 Chirality : 0.055 0.300 1564 Planarity : 0.006 0.070 1455 Dihedral : 19.034 178.481 3994 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.36 % Allowed : 19.85 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -5.27 (0.20), residues: 982 helix: -3.73 (0.17), residues: 421 sheet: -2.22 (0.51), residues: 98 loop : -3.52 (0.23), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 298 HIS 0.005 0.002 HIS A 586 PHE 0.024 0.002 PHE A1014 TYR 0.019 0.003 TYR A 584 ARG 0.006 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 59 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 486 TYR cc_start: 0.7549 (p90) cc_final: 0.6956 (p90) REVERT: A 739 MET cc_start: 0.8116 (mmm) cc_final: 0.7797 (mmt) REVERT: A 743 MET cc_start: 0.8116 (mmm) cc_final: 0.7620 (mmm) outliers start: 44 outliers final: 22 residues processed: 98 average time/residue: 0.2114 time to fit residues: 29.2718 Evaluate side-chains 68 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1063 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 94 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 249 GLN A 598 GLN A 781 ASN A 856 ASN A1031 ASN A1043 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9542 Z= 0.257 Angle : 0.654 7.593 13288 Z= 0.332 Chirality : 0.045 0.179 1564 Planarity : 0.005 0.054 1455 Dihedral : 18.716 170.639 2205 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.41 % Allowed : 20.46 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -4.17 (0.23), residues: 982 helix: -2.75 (0.21), residues: 432 sheet: -1.94 (0.53), residues: 98 loop : -2.92 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 PHE 0.030 0.002 PHE A 322 TYR 0.015 0.001 TYR A 643 ARG 0.006 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 50 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8796 (t) REVERT: A 214 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: A 264 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: A 486 TYR cc_start: 0.7619 (p90) cc_final: 0.7197 (p90) REVERT: A 743 MET cc_start: 0.8304 (mmm) cc_final: 0.7340 (mmm) REVERT: A 747 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: A 947 MET cc_start: 0.8607 (ttm) cc_final: 0.8301 (ttm) REVERT: A 1035 MET cc_start: 0.7387 (mmt) cc_final: 0.7164 (tpp) REVERT: A 1045 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7555 (mpp80) outliers start: 28 outliers final: 15 residues processed: 77 average time/residue: 0.2032 time to fit residues: 22.6924 Evaluate side-chains 63 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1045 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9542 Z= 0.149 Angle : 0.567 8.683 13288 Z= 0.282 Chirality : 0.041 0.175 1564 Planarity : 0.004 0.051 1455 Dihedral : 18.050 178.123 2186 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.56 % Allowed : 21.80 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -3.25 (0.25), residues: 982 helix: -1.99 (0.24), residues: 431 sheet: -2.02 (0.47), residues: 118 loop : -2.25 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 PHE 0.022 0.001 PHE A 322 TYR 0.012 0.001 TYR A 84 ARG 0.005 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8869 (mtp) cc_final: 0.8566 (mtt) REVERT: A 252 LYS cc_start: 0.8998 (tmmm) cc_final: 0.8656 (ttpp) REVERT: A 264 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: A 743 MET cc_start: 0.8273 (mmm) cc_final: 0.7563 (mmt) REVERT: A 947 MET cc_start: 0.8486 (ttm) cc_final: 0.8115 (ttm) REVERT: A 1045 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7460 (mpp80) outliers start: 21 outliers final: 12 residues processed: 75 average time/residue: 0.2117 time to fit residues: 23.0839 Evaluate side-chains 56 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1045 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 54.6258 > 50: distance: 58 - 93: 20.285 distance: 61 - 90: 13.118 distance: 79 - 82: 11.119 distance: 82 - 83: 7.486 distance: 83 - 84: 7.732 distance: 83 - 86: 8.262 distance: 84 - 85: 13.104 distance: 84 - 90: 10.736 distance: 87 - 88: 13.849 distance: 87 - 89: 4.505 distance: 90 - 91: 11.981 distance: 91 - 94: 13.275 distance: 92 - 93: 20.076 distance: 92 - 101: 13.817 distance: 94 - 95: 12.571 distance: 95 - 96: 15.923 distance: 95 - 97: 15.146 distance: 96 - 98: 12.828 distance: 97 - 99: 6.066 distance: 98 - 100: 11.385 distance: 99 - 100: 7.272 distance: 101 - 102: 17.244 distance: 102 - 103: 10.091 distance: 102 - 105: 35.459 distance: 103 - 104: 13.805 distance: 103 - 110: 20.640 distance: 105 - 106: 28.549 distance: 106 - 107: 8.368 distance: 107 - 108: 19.085 distance: 108 - 109: 32.791 distance: 110 - 111: 17.280 distance: 111 - 112: 22.458 distance: 111 - 114: 15.500 distance: 112 - 113: 19.784 distance: 112 - 117: 31.735 distance: 114 - 115: 13.638 distance: 114 - 116: 3.455 distance: 117 - 118: 12.212 distance: 118 - 119: 7.194 distance: 118 - 121: 14.431 distance: 119 - 120: 4.023 distance: 121 - 122: 21.495 distance: 122 - 123: 25.771 distance: 123 - 124: 6.262 distance: 123 - 125: 20.617 distance: 126 - 127: 21.820 distance: 127 - 128: 24.803 distance: 127 - 130: 7.891 distance: 128 - 129: 16.607 distance: 128 - 131: 12.731 distance: 131 - 132: 28.090 distance: 132 - 133: 14.926 distance: 132 - 135: 4.418 distance: 133 - 134: 6.161 distance: 133 - 136: 11.749 distance: 136 - 137: 18.360 distance: 137 - 138: 18.920 distance: 137 - 140: 18.316 distance: 138 - 139: 23.420 distance: 138 - 145: 17.879 distance: 140 - 141: 30.729 distance: 141 - 142: 14.603 distance: 142 - 143: 15.710 distance: 142 - 144: 24.273 distance: 146 - 147: 20.446 distance: 146 - 149: 39.096 distance: 147 - 148: 31.249 distance: 149 - 150: 14.032 distance: 150 - 151: 6.875 distance: 150 - 152: 22.937 distance: 153 - 154: 4.068 distance: 154 - 155: 11.490 distance: 154 - 157: 12.764 distance: 155 - 156: 7.783 distance: 155 - 165: 20.982 distance: 156 - 184: 30.079 distance: 157 - 158: 6.840 distance: 158 - 159: 12.094 distance: 158 - 160: 12.180 distance: 159 - 161: 24.158 distance: 160 - 162: 6.727 distance: 161 - 163: 6.209 distance: 162 - 163: 14.017 distance: 163 - 164: 5.502