Starting phenix.real_space_refine on Mon Sep 30 08:32:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/09_2024/5x58_6703.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 16102 2.51 5 N 4127 2.21 5 O 4904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8234 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8226 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Restraints were copied for chains: C Time building chain proxies: 26.56, per 1000 atoms: 1.05 Number of scatterers: 25265 At special positions: 0 Unit cell: (149.5, 139.1, 159.9, 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 132 16.00 O 4904 8.00 N 4127 7.00 C 16102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 691 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 357 " " NAG A1307 " - " ASN A 330 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 227 " " NAG A1311 " - " ASN A 158 " " NAG A1312 " - " ASN A 119 " " NAG A1313 " - " ASN A 65 " " NAG B1301 " - " ASN B 602 " " NAG B1302 " - " ASN B 691 " " NAG B1303 " - " ASN B 699 " " NAG B1304 " - " ASN B 783 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 357 " " NAG B1307 " - " ASN B 330 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 227 " " NAG B1311 " - " ASN B 158 " " NAG B1312 " - " ASN B 119 " " NAG B1313 " - " ASN B 65 " " NAG C1301 " - " ASN C 602 " " NAG C1302 " - " ASN C 691 " " NAG C1303 " - " ASN C 699 " " NAG C1304 " - " ASN C 783 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 357 " " NAG C1307 " - " ASN C 330 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 227 " " NAG C1311 " - " ASN C 158 " " NAG C1312 " - " ASN C 119 " " NAG C1313 " - " ASN C 65 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.583A pdb=" N GLY A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.694A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.170A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1014 removed outlier: 3.645A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.965A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.582A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 744 through 765 removed outlier: 4.109A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.584A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.811A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS C 929 " --> pdb=" O THR C 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 988 " --> pdb=" O GLN C 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 5.700A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER A 310 " --> pdb=" O ASN A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN A 321 " --> pdb=" O VAL A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 removed outlier: 6.097A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.524A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.743A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.598A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER B 310 " --> pdb=" O ASN B 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 652 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 38 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU C 216 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE2, first strand: chain 'C' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER C 310 " --> pdb=" O ASN C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.962A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 652 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2244 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: 10.34 Time building geometry restraints manager: 7.29 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: 7870 1.34 - 1.46: 5722 1.46 - 1.58: 12087 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25859 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 ... (remaining 25854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 34611 3.62 - 7.25: 513 7.25 - 10.87: 42 10.87 - 14.50: 15 14.50 - 18.12: 9 Bond angle restraints: 35190 Sorted by residual: angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.17 -9.26 1.17e+00 7.31e-01 6.27e+01 angle pdb=" N ARG C 306 " pdb=" CA ARG C 306 " pdb=" C ARG C 306 " ideal model delta sigma weight residual 110.91 120.13 -9.22 1.17e+00 7.31e-01 6.21e+01 angle pdb=" N ARG B 306 " pdb=" CA ARG B 306 " pdb=" C ARG B 306 " ideal model delta sigma weight residual 110.91 120.12 -9.21 1.17e+00 7.31e-01 6.20e+01 angle pdb=" N VAL B 354 " pdb=" CA VAL B 354 " pdb=" C VAL B 354 " ideal model delta sigma weight residual 110.72 103.92 6.80 1.01e+00 9.80e-01 4.53e+01 angle pdb=" N VAL C 354 " pdb=" CA VAL C 354 " pdb=" C VAL C 354 " ideal model delta sigma weight residual 110.72 103.94 6.78 1.01e+00 9.80e-01 4.51e+01 ... (remaining 35185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15186 21.67 - 43.34: 421 43.34 - 65.01: 100 65.01 - 86.68: 38 86.68 - 108.34: 90 Dihedral angle restraints: 15835 sinusoidal: 6613 harmonic: 9222 Sorted by residual: dihedral pdb=" CA THR B 616 " pdb=" C THR B 616 " pdb=" N PRO B 617 " pdb=" CA PRO B 617 " ideal model delta harmonic sigma weight residual 180.00 132.11 47.89 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA THR C 616 " pdb=" C THR C 616 " pdb=" N PRO C 617 " pdb=" CA PRO C 617 " ideal model delta harmonic sigma weight residual 180.00 132.17 47.83 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA THR A 616 " pdb=" C THR A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual 180.00 132.18 47.82 0 5.00e+00 4.00e-02 9.15e+01 ... (remaining 15832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3462 0.084 - 0.168: 551 0.168 - 0.252: 48 0.252 - 0.336: 17 0.336 - 0.420: 10 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CB ILE B 787 " pdb=" CA ILE B 787 " pdb=" CG1 ILE B 787 " pdb=" CG2 ILE B 787 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE C 787 " pdb=" CA ILE C 787 " pdb=" CG1 ILE C 787 " pdb=" CG2 ILE C 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 617 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.042 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 264 2.59 - 3.17: 20284 3.17 - 3.74: 38859 3.74 - 4.32: 55400 4.32 - 4.90: 88980 Nonbonded interactions: 203787 Sorted by model distance: nonbonded pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 467 " pdb=" SG CYS C 474 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS C 128 " pdb=" SG CYS C 159 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " model vdw 2.038 3.760 ... (remaining 203782 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 662 or resid 673 through 809 or resid 831 throu \ gh 1104 or resid 1302 through 1301)) selection = (chain 'B' and (resid 18 through 662 or resid 673 through 1104 or resid 1301 thr \ ough 1314)) selection = chain 'C' } 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: 1.460 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 68.870 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.007 0.090 25859 Z= 0.478 Angle : 1.173 18.125 35190 Z= 0.657 Chirality : 0.066 0.420 4088 Planarity : 0.006 0.075 4498 Dihedral : 14.958 108.345 9865 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 5.88 % Twisted General : 0.10 % 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: -4.64 (0.12), residues: 3135 helix: -4.02 (0.11), residues: 609 sheet: -2.43 (0.18), residues: 614 loop : -3.11 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 423 HIS 0.013 0.002 HIS C1030 PHE 0.024 0.003 PHE C 870 TYR 0.034 0.003 TYR B 481 ARG 0.012 0.001 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 692 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8744 (t0) cc_final: 0.8308 (m-30) REVERT: A 84 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8444 (tppt) REVERT: A 109 ASN cc_start: 0.7042 (p0) cc_final: 0.6251 (t0) REVERT: A 130 PHE cc_start: 0.7489 (m-80) cc_final: 0.6445 (m-80) REVERT: A 131 GLU cc_start: 0.6027 (tt0) cc_final: 0.5675 (pt0) REVERT: A 184 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8151 (mp0) REVERT: A 189 ASN cc_start: 0.8134 (t0) cc_final: 0.7691 (t0) REVERT: A 256 TYR cc_start: 0.8241 (m-80) cc_final: 0.8004 (m-80) REVERT: A 411 LYS cc_start: 0.7307 (tptm) cc_final: 0.6861 (tppt) REVERT: A 640 GLU cc_start: 0.8080 (tt0) cc_final: 0.7866 (tp30) REVERT: A 692 ASN cc_start: 0.8774 (m-40) cc_final: 0.8518 (p0) REVERT: A 707 GLU cc_start: 0.9144 (tt0) cc_final: 0.8920 (tt0) REVERT: A 733 ASN cc_start: 0.8794 (t160) cc_final: 0.8453 (m-40) REVERT: A 745 LEU cc_start: 0.8469 (tm) cc_final: 0.8115 (tp) REVERT: A 755 GLU cc_start: 0.8039 (pp20) cc_final: 0.7588 (mm-30) REVERT: A 762 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7894 (mm-30) REVERT: A 768 LYS cc_start: 0.8727 (tttp) cc_final: 0.8518 (tppt) REVERT: A 769 GLN cc_start: 0.8809 (pm20) cc_final: 0.8571 (pm20) REVERT: A 796 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7526 (mmtm) REVERT: A 833 CYS cc_start: 0.6335 (m) cc_final: 0.5736 (p) REVERT: A 851 MET cc_start: 0.8887 (mtt) cc_final: 0.8641 (mtm) REVERT: A 918 GLU cc_start: 0.8987 (tt0) cc_final: 0.8761 (mm-30) REVERT: A 963 LEU cc_start: 0.8200 (mm) cc_final: 0.7925 (mt) REVERT: A 970 GLU cc_start: 0.8255 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 972 GLU cc_start: 0.8453 (tt0) cc_final: 0.7826 (pp20) REVERT: A 1055 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8265 (ttm-80) REVERT: A 1071 PHE cc_start: 0.8032 (m-80) cc_final: 0.7759 (m-80) REVERT: B 57 ASP cc_start: 0.8731 (t0) cc_final: 0.8173 (m-30) REVERT: B 78 ASN cc_start: 0.7872 (p0) cc_final: 0.7662 (p0) REVERT: B 109 ASN cc_start: 0.7048 (p0) cc_final: 0.6204 (t0) REVERT: B 130 PHE cc_start: 0.7360 (m-80) cc_final: 0.7065 (m-80) REVERT: B 131 GLU cc_start: 0.5948 (tt0) cc_final: 0.5677 (pt0) REVERT: B 132 LEU cc_start: 0.6054 (mm) cc_final: 0.5692 (mm) REVERT: B 184 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7916 (mp0) REVERT: B 260 THR cc_start: 0.8990 (m) cc_final: 0.8767 (p) REVERT: B 410 TYR cc_start: 0.7792 (t80) cc_final: 0.7196 (t80) REVERT: B 447 LYS cc_start: 0.6739 (mttt) cc_final: 0.6497 (mmtm) REVERT: B 689 TYR cc_start: 0.7845 (t80) cc_final: 0.7641 (t80) REVERT: B 692 ASN cc_start: 0.8514 (m-40) cc_final: 0.8290 (p0) REVERT: B 693 THR cc_start: 0.8777 (p) cc_final: 0.8318 (p) REVERT: B 733 ASN cc_start: 0.8850 (t160) cc_final: 0.8473 (m-40) REVERT: B 745 LEU cc_start: 0.8634 (tm) cc_final: 0.7995 (mt) REVERT: B 746 ASN cc_start: 0.8705 (t0) cc_final: 0.8492 (t0) REVERT: B 755 GLU cc_start: 0.8148 (pp20) cc_final: 0.7731 (mm-30) REVERT: B 762 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8185 (mm-30) REVERT: B 796 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7399 (tppt) REVERT: B 851 MET cc_start: 0.8917 (mtt) cc_final: 0.8670 (mtm) REVERT: B 884 MET cc_start: 0.8788 (mmm) cc_final: 0.8463 (tpt) REVERT: B 886 TYR cc_start: 0.9018 (t80) cc_final: 0.8761 (t80) REVERT: B 897 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (m) REVERT: B 918 GLU cc_start: 0.9112 (tt0) cc_final: 0.8863 (mm-30) REVERT: B 972 GLU cc_start: 0.8579 (tt0) cc_final: 0.7986 (pt0) REVERT: B 1049 TYR cc_start: 0.8758 (t80) cc_final: 0.8486 (t80) REVERT: B 1054 GLU cc_start: 0.8820 (pm20) cc_final: 0.8282 (pm20) REVERT: B 1055 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8442 (ttm-80) REVERT: C 57 ASP cc_start: 0.8714 (t0) cc_final: 0.8253 (m-30) REVERT: C 101 TRP cc_start: 0.7736 (m-90) cc_final: 0.7500 (m-90) REVERT: C 109 ASN cc_start: 0.6946 (p0) cc_final: 0.6331 (t0) REVERT: C 131 GLU cc_start: 0.5825 (tt0) cc_final: 0.5220 (pt0) REVERT: C 132 LEU cc_start: 0.5754 (mm) cc_final: 0.5217 (mm) REVERT: C 184 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8357 (mp0) REVERT: C 207 ARG cc_start: 0.6166 (ptm160) cc_final: 0.5796 (mmt-90) REVERT: C 260 THR cc_start: 0.8946 (m) cc_final: 0.8598 (p) REVERT: C 340 TRP cc_start: 0.6175 (p-90) cc_final: 0.5553 (p-90) REVERT: C 411 LYS cc_start: 0.7242 (tptm) cc_final: 0.6839 (tppt) REVERT: C 518 ASP cc_start: 0.7451 (t70) cc_final: 0.7226 (p0) REVERT: C 560 ASP cc_start: 0.8526 (t70) cc_final: 0.8321 (t0) REVERT: C 733 ASN cc_start: 0.8678 (t160) cc_final: 0.8354 (m110) REVERT: C 745 LEU cc_start: 0.8476 (tm) cc_final: 0.8176 (mt) REVERT: C 746 ASN cc_start: 0.8739 (t0) cc_final: 0.8478 (t0) REVERT: C 755 GLU cc_start: 0.7836 (pp20) cc_final: 0.7505 (mm-30) REVERT: C 762 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8036 (mm-30) REVERT: C 768 LYS cc_start: 0.8611 (tttp) cc_final: 0.8334 (ttmm) REVERT: C 769 GLN cc_start: 0.8694 (pm20) cc_final: 0.8327 (pm20) REVERT: C 796 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7428 (mmtm) REVERT: C 900 GLU cc_start: 0.8735 (tt0) cc_final: 0.8495 (tt0) REVERT: C 918 GLU cc_start: 0.8972 (tt0) cc_final: 0.8757 (tm-30) REVERT: C 963 LEU cc_start: 0.8077 (mm) cc_final: 0.7733 (mt) REVERT: C 970 GLU cc_start: 0.8366 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 972 GLU cc_start: 0.8633 (tt0) cc_final: 0.8130 (tm-30) REVERT: C 1055 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8550 (ttm-80) REVERT: C 1071 PHE cc_start: 0.8060 (m-80) cc_final: 0.7773 (m-10) outliers start: 12 outliers final: 4 residues processed: 704 average time/residue: 0.3659 time to fit residues: 397.6915 Evaluate side-chains 409 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 405 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 920 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 127 optimal weight: 40.0000 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 286 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 112 GLN A 135 ASN A 201 GLN A 409 ASN A 522 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 599 GLN A 614 GLN A 632 GLN A 733 ASN A 766 GLN A 883 GLN A 904 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A 984 GLN A1090 ASN B 70 HIS B 135 ASN B 201 GLN B 280 GLN B 409 ASN B 522 ASN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 599 GLN B 614 GLN B 632 GLN B 733 ASN B 766 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 889 ASN B 904 GLN B 936 GLN B 937 ASN B 984 GLN B1053 GLN B1090 ASN C 70 HIS C 135 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 409 ASN C 492 GLN C 522 ASN C 526 ASN C 528 ASN C 614 GLN C 632 GLN C 733 ASN C 766 GLN C 835 GLN C 883 GLN C 896 ASN C 904 GLN C 936 GLN C 937 ASN C 984 GLN C1065 HIS ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25859 Z= 0.207 Angle : 0.737 13.556 35190 Z= 0.370 Chirality : 0.050 0.349 4088 Planarity : 0.005 0.073 4498 Dihedral : 13.035 82.702 4286 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.52 % Allowed : 10.41 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % 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: -3.36 (0.13), residues: 3135 helix: -1.55 (0.18), residues: 609 sheet: -1.73 (0.19), residues: 619 loop : -2.77 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 340 HIS 0.003 0.001 HIS B1046 PHE 0.026 0.002 PHE A 460 TYR 0.034 0.002 TYR A 481 ARG 0.006 0.001 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 486 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8401 (t0) cc_final: 0.8070 (m-30) REVERT: A 130 PHE cc_start: 0.7364 (m-80) cc_final: 0.6581 (m-80) REVERT: A 132 LEU cc_start: 0.5400 (mm) cc_final: 0.5087 (mm) REVERT: A 151 MET cc_start: 0.2791 (tpp) cc_final: 0.2127 (tmm) REVERT: A 184 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7979 (mp0) REVERT: A 316 PHE cc_start: 0.8184 (t80) cc_final: 0.7863 (t80) REVERT: A 342 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.6861 (ttm-80) REVERT: A 497 VAL cc_start: 0.8830 (t) cc_final: 0.8617 (p) REVERT: A 640 GLU cc_start: 0.8333 (tt0) cc_final: 0.8063 (tp30) REVERT: A 693 THR cc_start: 0.8475 (p) cc_final: 0.8051 (p) REVERT: A 733 ASN cc_start: 0.8651 (t0) cc_final: 0.8249 (m110) REVERT: A 745 LEU cc_start: 0.8502 (tm) cc_final: 0.8146 (mt) REVERT: A 755 GLU cc_start: 0.8354 (pp20) cc_final: 0.7875 (tp30) REVERT: A 762 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7878 (mm-30) REVERT: A 796 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7549 (mmtm) REVERT: A 833 CYS cc_start: 0.6686 (m) cc_final: 0.6034 (p) REVERT: A 918 GLU cc_start: 0.9027 (tt0) cc_final: 0.8774 (mm-30) REVERT: A 972 GLU cc_start: 0.8361 (tt0) cc_final: 0.7698 (pt0) REVERT: A 1055 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7948 (ttm-80) REVERT: B 57 ASP cc_start: 0.8479 (t0) cc_final: 0.8117 (m-30) REVERT: B 130 PHE cc_start: 0.7294 (m-80) cc_final: 0.6924 (m-80) REVERT: B 260 THR cc_start: 0.8900 (m) cc_final: 0.8519 (p) REVERT: B 342 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: B 410 TYR cc_start: 0.7430 (t80) cc_final: 0.7099 (t80) REVERT: B 447 LYS cc_start: 0.6745 (mttt) cc_final: 0.6282 (mmtm) REVERT: B 539 THR cc_start: 0.8003 (m) cc_final: 0.7518 (p) REVERT: B 689 TYR cc_start: 0.7693 (t80) cc_final: 0.7480 (t80) REVERT: B 692 ASN cc_start: 0.8590 (m-40) cc_final: 0.8378 (p0) REVERT: B 693 THR cc_start: 0.8700 (p) cc_final: 0.8122 (p) REVERT: B 730 GLU cc_start: 0.8381 (pm20) cc_final: 0.7717 (mm-30) REVERT: B 733 ASN cc_start: 0.8761 (t0) cc_final: 0.8296 (m-40) REVERT: B 755 GLU cc_start: 0.8303 (pp20) cc_final: 0.7718 (tp30) REVERT: B 762 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8090 (mm-30) REVERT: B 796 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7478 (tppt) REVERT: B 886 TYR cc_start: 0.8920 (t80) cc_final: 0.8681 (t80) REVERT: B 959 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (tm) REVERT: B 961 ASP cc_start: 0.7431 (m-30) cc_final: 0.7164 (m-30) REVERT: B 972 GLU cc_start: 0.8288 (tt0) cc_final: 0.7601 (pt0) REVERT: B 1054 GLU cc_start: 0.8638 (pm20) cc_final: 0.7998 (pm20) REVERT: B 1055 ARG cc_start: 0.8301 (mmm160) cc_final: 0.8031 (ttm-80) REVERT: B 1071 PHE cc_start: 0.7618 (m-80) cc_final: 0.7110 (m-80) REVERT: B 1095 GLN cc_start: 0.8464 (mm110) cc_final: 0.8257 (mm-40) REVERT: C 57 ASP cc_start: 0.8482 (t0) cc_final: 0.8051 (m-30) REVERT: C 78 ASN cc_start: 0.7838 (p0) cc_final: 0.7543 (p0) REVERT: C 131 GLU cc_start: 0.5844 (tt0) cc_final: 0.5622 (pt0) REVERT: C 207 ARG cc_start: 0.6300 (ptm160) cc_final: 0.5935 (mmt-90) REVERT: C 260 THR cc_start: 0.8925 (m) cc_final: 0.8479 (p) REVERT: C 305 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.5933 (m-80) REVERT: C 338 TYR cc_start: 0.7280 (p90) cc_final: 0.6736 (p90) REVERT: C 411 LYS cc_start: 0.7090 (tptm) cc_final: 0.6808 (tptp) REVERT: C 518 ASP cc_start: 0.7832 (t70) cc_final: 0.7455 (p0) REVERT: C 539 THR cc_start: 0.7891 (m) cc_final: 0.7339 (p) REVERT: C 599 GLN cc_start: 0.5935 (OUTLIER) cc_final: 0.5523 (mm-40) REVERT: C 733 ASN cc_start: 0.8626 (t0) cc_final: 0.8203 (m110) REVERT: C 734 LEU cc_start: 0.8712 (tp) cc_final: 0.8507 (tp) REVERT: C 745 LEU cc_start: 0.8702 (tm) cc_final: 0.8274 (mt) REVERT: C 755 GLU cc_start: 0.8213 (pp20) cc_final: 0.7682 (tp30) REVERT: C 762 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7994 (mm-30) REVERT: C 768 LYS cc_start: 0.8584 (tttp) cc_final: 0.8283 (tppp) REVERT: C 769 GLN cc_start: 0.8724 (pm20) cc_final: 0.8403 (pm20) REVERT: C 796 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7305 (tppt) REVERT: C 918 GLU cc_start: 0.9026 (tt0) cc_final: 0.8735 (tm-30) REVERT: C 961 ASP cc_start: 0.7466 (m-30) cc_final: 0.7176 (m-30) REVERT: C 963 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7486 (mt) REVERT: C 972 GLU cc_start: 0.8365 (tt0) cc_final: 0.7785 (pt0) REVERT: C 1054 GLU cc_start: 0.8687 (pm20) cc_final: 0.8280 (pp20) REVERT: C 1055 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8034 (ttm-80) REVERT: C 1071 PHE cc_start: 0.7494 (m-80) cc_final: 0.7117 (m-80) outliers start: 69 outliers final: 42 residues processed: 533 average time/residue: 0.3754 time to fit residues: 317.9271 Evaluate side-chains 432 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 386 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 60.8437 > 50: distance: 39 - 42: 8.170 distance: 40 - 41: 19.965 distance: 40 - 50: 10.382 distance: 42 - 43: 12.718 distance: 43 - 44: 16.050 distance: 43 - 45: 7.921 distance: 45 - 47: 4.127 distance: 46 - 48: 10.673 distance: 47 - 48: 6.856 distance: 48 - 49: 10.085 distance: 50 - 51: 13.298 distance: 51 - 52: 5.855 distance: 51 - 54: 6.737 distance: 52 - 53: 8.196 distance: 52 - 59: 7.300 distance: 54 - 55: 25.851 distance: 55 - 56: 20.570 distance: 56 - 57: 6.679 distance: 57 - 58: 21.184 distance: 59 - 60: 6.153 distance: 60 - 61: 12.747 distance: 60 - 63: 14.994 distance: 61 - 62: 15.744 distance: 61 - 66: 12.485 distance: 63 - 64: 22.084 distance: 63 - 65: 15.878 distance: 66 - 67: 9.634 distance: 66 - 72: 23.142 distance: 67 - 68: 13.309 distance: 67 - 70: 12.989 distance: 68 - 69: 17.624 distance: 68 - 73: 13.167 distance: 70 - 71: 10.077 distance: 71 - 72: 28.973 distance: 73 - 74: 10.014 distance: 74 - 75: 5.511 distance: 74 - 77: 10.164 distance: 75 - 76: 10.094 distance: 75 - 80: 6.494 distance: 77 - 78: 8.126 distance: 77 - 79: 13.494 distance: 80 - 81: 7.975 distance: 81 - 82: 6.601 distance: 81 - 84: 4.554 distance: 82 - 83: 3.891 distance: 82 - 88: 7.811 distance: 84 - 85: 11.146 distance: 85 - 86: 10.458 distance: 85 - 87: 12.400 distance: 88 - 89: 6.394 distance: 89 - 90: 10.199 distance: 89 - 92: 7.434 distance: 90 - 91: 19.106 distance: 90 - 97: 20.066 distance: 92 - 93: 6.274 distance: 93 - 94: 28.141 distance: 94 - 95: 42.439 distance: 95 - 96: 16.269 distance: 97 - 98: 9.761 distance: 98 - 99: 9.757 distance: 98 - 101: 12.195 distance: 99 - 100: 19.991 distance: 99 - 109: 14.468 distance: 101 - 102: 7.313 distance: 102 - 103: 10.336 distance: 102 - 104: 4.755 distance: 103 - 105: 4.749 distance: 104 - 106: 3.242 distance: 105 - 107: 6.556 distance: 106 - 107: 8.239 distance: 107 - 108: 4.654 distance: 109 - 110: 16.935 distance: 110 - 111: 24.801 distance: 110 - 113: 9.510 distance: 111 - 112: 46.205 distance: 111 - 120: 14.280 distance: 113 - 114: 7.094 distance: 114 - 115: 8.652 distance: 114 - 116: 11.541 distance: 115 - 117: 11.358 distance: 116 - 118: 8.725 distance: 117 - 119: 15.026 distance: 118 - 119: 14.754 distance: 120 - 121: 8.352 distance: 121 - 122: 23.368 distance: 122 - 123: 42.215 distance: 122 - 124: 15.575