Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 03:31:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbq_23741/05_2023/7mbq_23741.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Ca 8 9.91 5 S 176 5.16 5 C 20116 2.51 5 N 5160 2.21 5 O 5156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 453": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "A GLU 1045": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 994": "OE1" <-> "OE2" Residue "B GLU 1032": "OE1" <-> "OE2" Residue "B GLU 1045": "OE1" <-> "OE2" Residue "B GLU 1057": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C ARG 834": "NH1" <-> "NH2" Residue "C GLU 911": "OE1" <-> "OE2" Residue "C GLU 994": "OE1" <-> "OE2" Residue "C GLU 1032": "OE1" <-> "OE2" Residue "C GLU 1045": "OE1" <-> "OE2" Residue "C GLU 1057": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D ARG 496": "NH1" <-> "NH2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "D ARG 834": "NH1" <-> "NH2" Residue "D GLU 911": "OE1" <-> "OE2" Residue "D GLU 994": "OE1" <-> "OE2" Residue "D GLU 1032": "OE1" <-> "OE2" Residue "D GLU 1045": "OE1" <-> "OE2" Residue "D GLU 1057": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 30616 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 31, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 355 Chain: "B" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 31, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 355 Chain: "C" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 31, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 355 Chain: "D" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 31, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 355 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 15.68, per 1000 atoms: 0.51 Number of scatterers: 30616 At special positions: 0 Unit cell: (144.55, 144.55, 154.462, 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) Ca 8 19.99 S 176 16.00 O 5156 8.00 N 5160 7.00 C 20116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 921 " " NAG B1501 " - " ASN B 921 " " NAG C1501 " - " ASN C 921 " " NAG D3002 " - " ASN D 921 " Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 4.8 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 8 sheets defined 70.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.664A pdb=" N ASN A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.589A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 removed outlier: 3.671A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.812A pdb=" N GLN A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.508A pdb=" N ALA A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.509A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.961A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 812 Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 835 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 845 through 882 removed outlier: 3.848A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 903 removed outlier: 4.777A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.672A pdb=" N ILE A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 942 through 959 removed outlier: 3.550A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.865A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 997 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1062 Processing helix chain 'A' and resid 1063 through 1092 removed outlier: 3.524A pdb=" N MET A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.663A pdb=" N ASN B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.589A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 311 through 328 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.671A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.813A pdb=" N GLN B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.507A pdb=" N ALA B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 545 Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.509A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.960A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 812 Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 816 through 835 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 845 through 882 removed outlier: 3.848A pdb=" N ILE B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 850 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 864 " --> pdb=" O PHE B 860 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 removed outlier: 4.778A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix removed outlier: 3.671A pdb=" N ILE B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 942 through 959 removed outlier: 3.550A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 979 removed outlier: 3.865A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 997 Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1062 Processing helix chain 'B' and resid 1063 through 1092 removed outlier: 3.525A pdb=" N MET B1092 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.065A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.664A pdb=" N ASN C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.588A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 311 through 328 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.670A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 460 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.814A pdb=" N GLN C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.508A pdb=" N ALA C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 545 Processing helix chain 'C' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.510A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.961A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 812 Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 816 through 835 Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 845 through 882 removed outlier: 3.847A pdb=" N ILE C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 850 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 864 " --> pdb=" O PHE C 860 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 865 " --> pdb=" O PHE C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 903 removed outlier: 4.777A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix removed outlier: 3.671A pdb=" N ILE C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 942 through 959 removed outlier: 3.550A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 979 removed outlier: 3.867A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 997 Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.935A pdb=" N SER C1009 " --> pdb=" O PHE C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1062 Processing helix chain 'C' and resid 1063 through 1092 removed outlier: 3.524A pdb=" N MET C1092 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.663A pdb=" N ASN D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.588A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 311 through 328 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.671A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 499 through 511 removed outlier: 3.813A pdb=" N GLN D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.507A pdb=" N ALA D 517 " --> pdb=" O ARG D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 545 Processing helix chain 'D' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 574 Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.510A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.961A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 812 Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 816 through 835 Processing helix chain 'D' and resid 836 through 842 Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.848A pdb=" N ILE D 849 " --> pdb=" O LEU D 845 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 850 " --> pdb=" O GLY D 846 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE D 864 " --> pdb=" O PHE D 860 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE D 865 " --> pdb=" O PHE D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 903 removed outlier: 4.778A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix removed outlier: 3.671A pdb=" N ILE D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 912 Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 942 through 959 removed outlier: 3.551A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 979 removed outlier: 3.865A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 997 Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER D1009 " --> pdb=" O PHE D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1062 Processing helix chain 'D' and resid 1063 through 1092 removed outlier: 3.524A pdb=" N MET D1092 " --> pdb=" O GLN D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.636A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 173 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU A 241 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 217 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 219 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.637A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 173 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 241 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS B 217 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 243 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU B 219 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.637A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS C 173 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 241 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 217 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU C 243 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU C 219 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 205 Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.636A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS D 173 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU D 241 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS D 217 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU D 243 " --> pdb=" O CYS D 217 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 202 through 205 2072 hydrogen bonds defined for protein. 6060 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: 12.21 Time building geometry restraints manager: 13.24 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: 9429 1.34 - 1.46: 5385 1.46 - 1.58: 16290 1.58 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 31396 Sorted by residual: bond pdb=" C3 NAG B1501 " pdb=" O3 NAG B1501 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C3 NAG D3002 " pdb=" O3 NAG D3002 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C3 NAG C1501 " pdb=" O3 NAG C1501 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C3 NAG A1501 " pdb=" O3 NAG A1501 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG A1501 " pdb=" O5 NAG A1501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 31391 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.24: 891 106.24 - 113.20: 17784 113.20 - 120.16: 10456 120.16 - 127.12: 13390 127.12 - 134.09: 407 Bond angle restraints: 42928 Sorted by residual: angle pdb=" N GLN D 511 " pdb=" CA GLN D 511 " pdb=" C GLN D 511 " ideal model delta sigma weight residual 112.59 118.40 -5.81 1.22e+00 6.72e-01 2.27e+01 angle pdb=" N GLN C 511 " pdb=" CA GLN C 511 " pdb=" C GLN C 511 " ideal model delta sigma weight residual 112.59 118.39 -5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" N GLN A 511 " pdb=" CA GLN A 511 " pdb=" C GLN A 511 " ideal model delta sigma weight residual 112.59 118.38 -5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" N GLN B 511 " pdb=" CA GLN B 511 " pdb=" C GLN B 511 " ideal model delta sigma weight residual 112.59 118.36 -5.77 1.22e+00 6.72e-01 2.24e+01 angle pdb=" N ARG D 513 " pdb=" CA ARG D 513 " pdb=" C ARG D 513 " ideal model delta sigma weight residual 108.41 101.11 7.30 1.61e+00 3.86e-01 2.06e+01 ... (remaining 42923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16221 17.58 - 35.17: 1559 35.17 - 52.75: 348 52.75 - 70.34: 88 70.34 - 87.92: 20 Dihedral angle restraints: 18236 sinusoidal: 6556 harmonic: 11680 Sorted by residual: dihedral pdb=" CA LEU A 544 " pdb=" C LEU A 544 " pdb=" N ALA A 545 " pdb=" CA ALA A 545 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 544 " pdb=" C LEU C 544 " pdb=" N ALA C 545 " pdb=" CA ALA C 545 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU D 544 " pdb=" C LEU D 544 " pdb=" N ALA D 545 " pdb=" CA ALA D 545 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 18233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4392 0.057 - 0.114: 685 0.114 - 0.170: 31 0.170 - 0.227: 8 0.227 - 0.284: 16 Chirality restraints: 5132 Sorted by residual: chirality pdb=" C41 YUY D3001 " pdb=" C40 YUY D3001 " pdb=" C42 YUY D3001 " pdb=" O7 YUY D3001 " both_signs ideal model delta sigma weight residual False -2.21 -2.50 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN A 512 " pdb=" N ASN A 512 " pdb=" C ASN A 512 " pdb=" CB ASN A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C41 YUY B1505 " pdb=" C40 YUY B1505 " pdb=" C42 YUY B1505 " pdb=" O7 YUY B1505 " both_signs ideal model delta sigma weight residual False -2.21 -2.49 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5129 not shown) Planarity restraints: 5240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " 0.037 2.00e-02 2.50e+03 3.08e-02 1.18e+01 pdb=" C7 NAG C1501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " -0.048 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D3002 " 0.037 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" C7 NAG D3002 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D3002 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG D3002 " -0.048 2.00e-02 2.50e+03 pdb=" O7 NAG D3002 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1501 " 0.037 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C7 NAG A1501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG A1501 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1501 " -0.048 2.00e-02 2.50e+03 pdb=" O7 NAG A1501 " -0.007 2.00e-02 2.50e+03 ... (remaining 5237 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6276 2.78 - 3.31: 29990 3.31 - 3.84: 54255 3.84 - 4.37: 61822 4.37 - 4.90: 105283 Nonbonded interactions: 257626 Sorted by model distance: nonbonded pdb=" O GLN C 771 " pdb=" OG1 THR C 775 " model vdw 2.246 2.440 nonbonded pdb=" O GLN B 771 " pdb=" OG1 THR B 775 " model vdw 2.246 2.440 nonbonded pdb=" O GLN A 771 " pdb=" OG1 THR A 775 " model vdw 2.246 2.440 nonbonded pdb=" O GLN D 771 " pdb=" OG1 THR D 775 " model vdw 2.247 2.440 nonbonded pdb=" NE2 GLN C 906 " pdb=" O HOH C1601 " model vdw 2.266 2.520 ... (remaining 257621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1092 or resid 1503)) selection = (chain 'B' and (resid 16 through 1092 or resid 1503)) selection = (chain 'C' and (resid 16 through 1092 or resid 1503)) selection = (chain 'D' and (resid 16 through 1092 or resid 3003)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.440 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: 0.030 Extract box with map and model: 28.400 Check model and map are aligned: 0.490 Set scattering table: 0.270 Process input model: 78.140 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.003 0.033 31396 Z= 0.214 Angle : 0.589 8.003 42928 Z= 0.337 Chirality : 0.042 0.284 5132 Planarity : 0.005 0.077 5236 Dihedral : 15.268 87.924 10636 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.14), residues: 3944 helix: 2.03 (0.10), residues: 2576 sheet: 0.43 (0.32), residues: 308 loop : -0.67 (0.20), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 3.812 Fit side-chains outliers start: 17 outliers final: 0 residues processed: 203 average time/residue: 1.6702 time to fit residues: 392.4517 Evaluate side-chains 152 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.8980 chunk 300 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 202 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 310 optimal weight: 0.3980 chunk 120 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: