Starting phenix.real_space_refine on Fri Jan 24 03:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrc_34967/01_2025/8hrc_34967_neut.cif" } resolution = 2.58 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= 0.005 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 384 5.16 5 C 48012 2.51 5 N 13032 2.21 5 O 13536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 74964 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "I" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 29.75, per 1000 atoms: 0.40 Number of scatterers: 74964 At special positions: 0 Unit cell: (213.2, 213.2, 213.2, 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 384 16.00 O 13536 8.00 N 13032 7.00 C 48012 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 - 3.00 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=0, symmetry=0 Time building additional restraints: 13.57 Conformation dependent library (CDL) restraints added in 7.0 seconds 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17784 Finding SS restraints... Secondary structure from input PDB file: 492 helices and 72 sheets defined 64.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 45 through 63 Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 224 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 243 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 285 through 311 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 436 through 456 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 505 through 520 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 593 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 619 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 756 through 771 Processing helix chain 'A' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 224 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN B 242 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 243 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 285 through 311 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 385 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 436 through 456 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 619 Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 662 through 671 Processing helix chain 'B' and resid 681 through 699 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 756 through 771 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 45 through 63 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 200 through 224 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN C 242 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 243 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 285 through 311 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 436 through 456 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 476 through 479 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 553 through 568 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 593 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 613 through 619 Processing helix chain 'C' and resid 632 through 644 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 662 through 671 Processing helix chain 'C' and resid 681 through 699 Processing helix chain 'C' and resid 718 through 722 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 756 through 771 Processing helix chain 'C' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY C 790 " --> pdb=" O VAL C 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 25 through 41 Processing helix chain 'D' and resid 45 through 63 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 200 through 224 Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN D 242 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 243 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 285 through 311 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 385 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 476 through 479 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 553 through 568 Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 573 through 593 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 613 through 619 Processing helix chain 'D' and resid 632 through 644 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 681 through 699 Processing helix chain 'D' and resid 718 through 722 Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 756 through 771 Processing helix chain 'D' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 45 through 63 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 94 through 103 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 200 through 224 Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA E 232 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN E 242 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER E 243 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 285 through 311 Processing helix chain 'E' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 385 Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'E' and resid 436 through 456 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 476 through 479 Processing helix chain 'E' and resid 480 through 489 Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 553 through 568 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 593 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 613 through 619 Processing helix chain 'E' and resid 632 through 644 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 662 through 671 Processing helix chain 'E' and resid 681 through 699 Processing helix chain 'E' and resid 718 through 722 Processing helix chain 'E' and resid 723 through 728 Processing helix chain 'E' and resid 756 through 771 Processing helix chain 'E' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY E 790 " --> pdb=" O VAL E 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG E 791 " --> pdb=" O ASN E 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 8 through 17 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 45 through 63 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 107 through 118 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 200 through 224 Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA F 232 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN F 242 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 243 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 285 through 311 Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 3.843A pdb=" N TYR F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 385 Processing helix chain 'F' and resid 396 through 405 Processing helix chain 'F' and resid 436 through 456 Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 476 through 479 Processing helix chain 'F' and resid 480 through 489 Processing helix chain 'F' and resid 505 through 520 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 553 through 568 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'F' and resid 613 through 619 Processing helix chain 'F' and resid 632 through 644 Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 662 through 671 Processing helix chain 'F' and resid 681 through 699 Processing helix chain 'F' and resid 718 through 722 Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 756 through 771 Processing helix chain 'F' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY F 790 " --> pdb=" O VAL F 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 25 through 41 Processing helix chain 'G' and resid 45 through 63 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 136 through 146 Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 185 through 196 Processing helix chain 'G' and resid 200 through 224 Processing helix chain 'G' and resid 229 through 233 removed outlier: 3.713A pdb=" N ALA G 232 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN G 242 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 243 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 285 through 311 Processing helix chain 'G' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 385 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 436 through 456 Processing helix chain 'G' and resid 457 through 462 Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 489 Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 553 through 568 Processing helix chain 'G' and resid 570 through 572 No H-bonds generated for 'chain 'G' and resid 570 through 572' Processing helix chain 'G' and resid 573 through 593 Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 610 through 612 No H-bonds generated for 'chain 'G' and resid 610 through 612' Processing helix chain 'G' and resid 613 through 619 Processing helix chain 'G' and resid 632 through 644 Processing helix chain 'G' and resid 650 through 661 Processing helix chain 'G' and resid 662 through 671 Processing helix chain 'G' and resid 681 through 699 Processing helix chain 'G' and resid 718 through 722 Processing helix chain 'G' and resid 723 through 728 Processing helix chain 'G' and resid 756 through 771 Processing helix chain 'G' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY G 790 " --> pdb=" O VAL G 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG G 791 " --> pdb=" O ASN G 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 8 through 17 Processing helix chain 'H' and resid 25 through 41 Processing helix chain 'H' and resid 45 through 63 Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 107 through 118 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 184 Processing helix chain 'H' and resid 185 through 196 Processing helix chain 'H' and resid 200 through 224 Processing helix chain 'H' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN H 242 " --> pdb=" O GLN H 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER H 243 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 280 Processing helix chain 'H' and resid 285 through 311 Processing helix chain 'H' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 343 removed outlier: 3.843A pdb=" N TYR H 334 " --> pdb=" O THR H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 385 Processing helix chain 'H' and resid 396 through 405 Processing helix chain 'H' and resid 436 through 456 Processing helix chain 'H' and resid 457 through 462 Processing helix chain 'H' and resid 476 through 479 Processing helix chain 'H' and resid 480 through 489 Processing helix chain 'H' and resid 505 through 520 Processing helix chain 'H' and resid 537 through 542 Processing helix chain 'H' and resid 553 through 568 Processing helix chain 'H' and resid 570 through 572 No H-bonds generated for 'chain 'H' and resid 570 through 572' Processing helix chain 'H' and resid 573 through 593 Processing helix chain 'H' and resid 599 through 609 Processing helix chain 'H' and resid 610 through 612 No H-bonds generated for 'chain 'H' and resid 610 through 612' Processing helix chain 'H' and resid 613 through 619 Processing helix chain 'H' and resid 632 through 644 Processing helix chain 'H' and resid 650 through 661 Processing helix chain 'H' and resid 662 through 671 Processing helix chain 'H' and resid 681 through 699 Processing helix chain 'H' and resid 718 through 722 Processing helix chain 'H' and resid 723 through 728 Processing helix chain 'H' and resid 756 through 771 Processing helix chain 'H' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY H 790 " --> pdb=" O VAL H 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG H 791 " --> pdb=" O ASN H 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 8 through 17 Processing helix chain 'I' and resid 25 through 41 Processing helix chain 'I' and resid 45 through 63 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 184 Processing helix chain 'I' and resid 185 through 196 Processing helix chain 'I' and resid 200 through 224 Processing helix chain 'I' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA I 232 " --> pdb=" O GLU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN I 242 " --> pdb=" O GLN I 239 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER I 243 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 285 through 311 Processing helix chain 'I' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR I 334 " --> pdb=" O THR I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 385 Processing helix chain 'I' and resid 396 through 405 Processing helix chain 'I' and resid 436 through 456 Processing helix chain 'I' and resid 457 through 462 Processing helix chain 'I' and resid 476 through 479 Processing helix chain 'I' and resid 480 through 489 Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 537 through 542 Processing helix chain 'I' and resid 553 through 568 Processing helix chain 'I' and resid 570 through 572 No H-bonds generated for 'chain 'I' and resid 570 through 572' Processing helix chain 'I' and resid 573 through 593 Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 613 through 619 Processing helix chain 'I' and resid 632 through 644 Processing helix chain 'I' and resid 650 through 661 Processing helix chain 'I' and resid 662 through 671 Processing helix chain 'I' and resid 681 through 699 Processing helix chain 'I' and resid 718 through 722 Processing helix chain 'I' and resid 723 through 728 Processing helix chain 'I' and resid 756 through 771 Processing helix chain 'I' and resid 775 through 793 removed outlier: 3.773A pdb=" N GLY I 790 " --> pdb=" O VAL I 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 791 " --> pdb=" O ASN I 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 8 through 17 Processing helix chain 'J' and resid 25 through 41 Processing helix chain 'J' and resid 45 through 63 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 94 through 103 Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 136 through 146 Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 184 Processing helix chain 'J' and resid 185 through 196 Processing helix chain 'J' and resid 200 through 224 Processing helix chain 'J' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA J 232 " --> pdb=" O GLU J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN J 242 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER J 243 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 285 through 311 Processing helix chain 'J' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU J 329 " --> pdb=" O GLU J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR J 334 " --> pdb=" O THR J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 385 Processing helix chain 'J' and resid 396 through 405 Processing helix chain 'J' and resid 436 through 456 Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 476 through 479 Processing helix chain 'J' and resid 480 through 489 Processing helix chain 'J' and resid 505 through 520 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 553 through 568 Processing helix chain 'J' and resid 570 through 572 No H-bonds generated for 'chain 'J' and resid 570 through 572' Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 599 through 609 Processing helix chain 'J' and resid 610 through 612 No H-bonds generated for 'chain 'J' and resid 610 through 612' Processing helix chain 'J' and resid 613 through 619 Processing helix chain 'J' and resid 632 through 644 Processing helix chain 'J' and resid 650 through 661 Processing helix chain 'J' and resid 662 through 671 Processing helix chain 'J' and resid 681 through 699 Processing helix chain 'J' and resid 718 through 722 Processing helix chain 'J' and resid 723 through 728 Processing helix chain 'J' and resid 756 through 771 Processing helix chain 'J' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY J 790 " --> pdb=" O VAL J 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 45 through 63 Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 120 through 124 Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 184 Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 200 through 224 Processing helix chain 'K' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA K 232 " --> pdb=" O GLU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER K 243 " --> pdb=" O LEU K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 280 Processing helix chain 'K' and resid 285 through 311 Processing helix chain 'K' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU K 329 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR K 334 " --> pdb=" O THR K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 385 Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'K' and resid 436 through 456 Processing helix chain 'K' and resid 457 through 462 Processing helix chain 'K' and resid 476 through 479 Processing helix chain 'K' and resid 480 through 489 Processing helix chain 'K' and resid 505 through 520 Processing helix chain 'K' and resid 537 through 542 Processing helix chain 'K' and resid 553 through 568 Processing helix chain 'K' and resid 570 through 572 No H-bonds generated for 'chain 'K' and resid 570 through 572' Processing helix chain 'K' and resid 573 through 593 Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 610 through 612 No H-bonds generated for 'chain 'K' and resid 610 through 612' Processing helix chain 'K' and resid 613 through 619 Processing helix chain 'K' and resid 632 through 644 Processing helix chain 'K' and resid 650 through 661 Processing helix chain 'K' and resid 662 through 671 Processing helix chain 'K' and resid 681 through 699 Processing helix chain 'K' and resid 718 through 722 Processing helix chain 'K' and resid 723 through 728 Processing helix chain 'K' and resid 756 through 771 Processing helix chain 'K' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY K 790 " --> pdb=" O VAL K 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG K 791 " --> pdb=" O ASN K 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 8 through 17 Processing helix chain 'L' and resid 25 through 41 Processing helix chain 'L' and resid 45 through 63 Processing helix chain 'L' and resid 68 through 80 Processing helix chain 'L' and resid 94 through 103 Processing helix chain 'L' and resid 107 through 118 Processing helix chain 'L' and resid 120 through 124 Processing helix chain 'L' and resid 136 through 146 Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 184 Processing helix chain 'L' and resid 185 through 196 Processing helix chain 'L' and resid 200 through 224 Processing helix chain 'L' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA L 232 " --> pdb=" O GLU L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN L 242 " --> pdb=" O GLN L 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER L 243 " --> pdb=" O LEU L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 280 Processing helix chain 'L' and resid 285 through 311 Processing helix chain 'L' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU L 329 " --> pdb=" O GLU L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR L 334 " --> pdb=" O THR L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 385 Processing helix chain 'L' and resid 396 through 405 Processing helix chain 'L' and resid 436 through 456 Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 480 through 489 Processing helix chain 'L' and resid 505 through 520 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 553 through 568 Processing helix chain 'L' and resid 570 through 572 No H-bonds generated for 'chain 'L' and resid 570 through 572' Processing helix chain 'L' and resid 573 through 593 Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 610 through 612 No H-bonds generated for 'chain 'L' and resid 610 through 612' Processing helix chain 'L' and resid 613 through 619 Processing helix chain 'L' and resid 632 through 644 Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 681 through 699 Processing helix chain 'L' and resid 718 through 722 Processing helix chain 'L' and resid 723 through 728 Processing helix chain 'L' and resid 756 through 771 Processing helix chain 'L' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY L 790 " --> pdb=" O VAL L 786 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS A 149 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU A 354 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 151 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG A 356 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A 153 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 351 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA A 417 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 353 " --> pdb=" O ALA A 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 Processing sheet with id=AA5, first strand: chain 'A' and resid 496 through 498 removed outlier: 6.660A pdb=" N TYR A 497 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 703 " --> pdb=" O CYS A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 552 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS B 149 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 354 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 151 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG B 356 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN B 153 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 351 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA B 417 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 353 " --> pdb=" O ALA B 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AB1, first strand: chain 'B' and resid 421 through 422 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.657A pdb=" N TYR B 497 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 703 " --> pdb=" O CYS B 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 548 through 552 Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 84 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS C 149 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU C 354 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR C 151 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 356 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN C 153 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 351 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA C 417 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 353 " --> pdb=" O ALA C 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.665A pdb=" N TYR C 497 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 703 " --> pdb=" O CYS C 744 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 548 through 552 Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC2, first strand: chain 'D' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS D 149 " --> pdb=" O TYR D 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU D 354 " --> pdb=" O HIS D 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR D 151 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG D 356 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN D 153 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG D 351 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA D 417 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 353 " --> pdb=" O ALA D 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AC4, first strand: chain 'D' and resid 421 through 422 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 6.648A pdb=" N TYR D 497 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 703 " --> pdb=" O CYS D 744 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AC7, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC8, first strand: chain 'E' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS E 149 " --> pdb=" O TYR E 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU E 354 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR E 151 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 356 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN E 153 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 351 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 417 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 353 " --> pdb=" O ALA E 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 245 through 247 Processing sheet with id=AD1, first strand: chain 'E' and resid 421 through 422 Processing sheet with id=AD2, first strand: chain 'E' and resid 496 through 498 removed outlier: 6.666A pdb=" N TYR E 497 " --> pdb=" O GLY E 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 703 " --> pdb=" O CYS E 744 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 548 through 552 Processing sheet with id=AD4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD5, first strand: chain 'F' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS F 149 " --> pdb=" O TYR F 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU F 354 " --> pdb=" O HIS F 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR F 151 " --> pdb=" O GLU F 354 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG F 356 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN F 153 " --> pdb=" O ARG F 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG F 351 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA F 417 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 353 " --> pdb=" O ALA F 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 245 through 247 Processing sheet with id=AD7, first strand: chain 'F' and resid 421 through 422 Processing sheet with id=AD8, first strand: chain 'F' and resid 496 through 498 removed outlier: 6.654A pdb=" N TYR F 497 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 703 " --> pdb=" O CYS F 744 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 548 through 552 Processing sheet with id=AE1, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AE2, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG G 351 " --> pdb=" O GLU G 415 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA G 417 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU G 353 " --> pdb=" O ALA G 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 245 through 247 Processing sheet with id=AE4, first strand: chain 'G' and resid 421 through 422 Processing sheet with id=AE5, first strand: chain 'G' and resid 496 through 498 removed outlier: 6.669A pdb=" N TYR G 497 " --> pdb=" O GLY G 529 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE G 703 " --> pdb=" O CYS G 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 548 through 552 Processing sheet with id=AE7, first strand: chain 'H' and resid 81 through 84 Processing sheet with id=AE8, first strand: chain 'H' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS H 149 " --> pdb=" O TYR H 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU H 354 " --> pdb=" O HIS H 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR H 151 " --> pdb=" O GLU H 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG H 356 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN H 153 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG H 351 " --> pdb=" O GLU H 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA H 417 " --> pdb=" O ARG H 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 353 " --> pdb=" O ALA H 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 245 through 247 Processing sheet with id=AF1, first strand: chain 'H' and resid 421 through 422 Processing sheet with id=AF2, first strand: chain 'H' and resid 496 through 498 removed outlier: 6.651A pdb=" N TYR H 497 " --> pdb=" O GLY H 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE H 703 " --> pdb=" O CYS H 744 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 548 through 552 Processing sheet with id=AF4, first strand: chain 'I' and resid 81 through 84 Processing sheet with id=AF5, first strand: chain 'I' and resid 148 through 154 removed outlier: 4.684A pdb=" N HIS I 149 " --> pdb=" O TYR I 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU I 354 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR I 151 " --> pdb=" O GLU I 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG I 356 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN I 153 " --> pdb=" O ARG I 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG I 351 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA I 417 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 353 " --> pdb=" O ALA I 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 245 through 247 Processing sheet with id=AF7, first strand: chain 'I' and resid 421 through 422 Processing sheet with id=AF8, first strand: chain 'I' and resid 496 through 498 removed outlier: 6.645A pdb=" N TYR I 497 " --> pdb=" O GLY I 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE I 703 " --> pdb=" O CYS I 744 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 548 through 552 Processing sheet with id=AG1, first strand: chain 'J' and resid 81 through 84 Processing sheet with id=AG2, first strand: chain 'J' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS J 149 " --> pdb=" O TYR J 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU J 354 " --> pdb=" O HIS J 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR J 151 " --> pdb=" O GLU J 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG J 356 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN J 153 " --> pdb=" O ARG J 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG J 351 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA J 417 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 353 " --> pdb=" O ALA J 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 245 through 247 Processing sheet with id=AG4, first strand: chain 'J' and resid 421 through 422 Processing sheet with id=AG5, first strand: chain 'J' and resid 496 through 498 removed outlier: 6.648A pdb=" N TYR J 497 " --> pdb=" O GLY J 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE J 703 " --> pdb=" O CYS J 744 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 548 through 552 Processing sheet with id=AG7, first strand: chain 'K' and resid 81 through 84 Processing sheet with id=AG8, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.684A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG K 351 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA K 417 " --> pdb=" O ARG K 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 353 " --> pdb=" O ALA K 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 245 through 247 Processing sheet with id=AH1, first strand: chain 'K' and resid 421 through 422 Processing sheet with id=AH2, first strand: chain 'K' and resid 496 through 498 removed outlier: 6.664A pdb=" N TYR K 497 " --> pdb=" O GLY K 529 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE K 703 " --> pdb=" O CYS K 744 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 548 through 552 Processing sheet with id=AH4, first strand: chain 'L' and resid 81 through 84 Processing sheet with id=AH5, first strand: chain 'L' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS L 149 " --> pdb=" O TYR L 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU L 354 " --> pdb=" O HIS L 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR L 151 " --> pdb=" O GLU L 354 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG L 356 " --> pdb=" O THR L 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN L 153 " --> pdb=" O ARG L 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG L 351 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA L 417 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 353 " --> pdb=" O ALA L 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 245 through 247 Processing sheet with id=AH7, first strand: chain 'L' and resid 421 through 422 Processing sheet with id=AH8, first strand: chain 'L' and resid 496 through 498 removed outlier: 6.664A pdb=" N TYR L 497 " --> pdb=" O GLY L 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE L 703 " --> pdb=" O CYS L 744 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 548 through 552 4225 hydrogen bonds defined for protein. 12135 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: 34.94 Time building geometry restraints manager: 16.28 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: 24551 1.34 - 1.46: 12310 1.46 - 1.58: 39375 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 76836 Sorted by residual: bond pdb=" N VAL E 499 " pdb=" CA VAL E 499 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.22e-02 6.72e+03 6.84e+00 bond pdb=" N VAL L 499 " pdb=" CA VAL L 499 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.22e-02 6.72e+03 6.79e+00 bond pdb=" N VAL G 499 " pdb=" CA VAL G 499 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.22e-02 6.72e+03 6.52e+00 bond pdb=" N VAL C 499 " pdb=" CA VAL C 499 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.23e-02 6.61e+03 6.46e+00 bond pdb=" N VAL B 499 " pdb=" CA VAL B 499 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.23e-02 6.61e+03 6.44e+00 ... (remaining 76831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 103100 2.05 - 4.10: 967 4.10 - 6.15: 105 6.15 - 8.20: 12 8.20 - 10.25: 12 Bond angle restraints: 104196 Sorted by residual: angle pdb=" CA ARG I 575 " pdb=" CB ARG I 575 " pdb=" CG ARG I 575 " ideal model delta sigma weight residual 114.10 124.35 -10.25 2.00e+00 2.50e-01 2.63e+01 angle pdb=" CA ARG D 575 " pdb=" CB ARG D 575 " pdb=" CG ARG D 575 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG F 575 " pdb=" CB ARG F 575 " pdb=" CG ARG F 575 " ideal model delta sigma weight residual 114.10 124.33 -10.23 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG K 575 " pdb=" CB ARG K 575 " pdb=" CG ARG K 575 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 angle pdb=" CA ARG E 575 " pdb=" CB ARG E 575 " pdb=" CG ARG E 575 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 ... (remaining 104191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 42308 17.45 - 34.89: 3137 34.89 - 52.34: 656 52.34 - 69.79: 135 69.79 - 87.23: 120 Dihedral angle restraints: 46356 sinusoidal: 18984 harmonic: 27372 Sorted by residual: dihedral pdb=" CA LEU B 574 " pdb=" C LEU B 574 " pdb=" N ARG B 575 " pdb=" CA ARG B 575 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU F 574 " pdb=" C LEU F 574 " pdb=" N ARG F 575 " pdb=" CA ARG F 575 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU E 574 " pdb=" C LEU E 574 " pdb=" N ARG E 575 " pdb=" CA ARG E 575 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 46353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 9255 0.047 - 0.093: 1723 0.093 - 0.140: 382 0.140 - 0.186: 4 0.186 - 0.233: 12 Chirality restraints: 11376 Sorted by residual: chirality pdb=" CA VAL B 499 " pdb=" N VAL B 499 " pdb=" C VAL B 499 " pdb=" CB VAL B 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL F 499 " pdb=" N VAL F 499 " pdb=" C VAL F 499 " pdb=" CB VAL F 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 499 " pdb=" N VAL A 499 " pdb=" C VAL A 499 " pdb=" CB VAL A 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 11373 not shown) Planarity restraints: 13368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 236 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO I 237 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 237 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 237 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 236 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO J 237 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 237 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 237 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 236 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 237 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 237 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 237 " 0.025 5.00e-02 4.00e+02 ... (remaining 13365 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13312 2.77 - 3.30: 73528 3.30 - 3.83: 133908 3.83 - 4.37: 161802 4.37 - 4.90: 265669 Nonbonded interactions: 648219 Sorted by model distance: nonbonded pdb=" O THR E 100 " pdb=" OG SER E 103 " model vdw 2.237 3.040 nonbonded pdb=" O THR G 100 " pdb=" OG SER G 103 " model vdw 2.237 3.040 nonbonded pdb=" O THR J 100 " pdb=" OG SER J 103 " model vdw 2.237 3.040 nonbonded pdb=" O THR C 100 " pdb=" OG SER C 103 " model vdw 2.237 3.040 nonbonded pdb=" O THR H 100 " pdb=" OG SER H 103 " model vdw 2.237 3.040 ... (remaining 648214 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: 0.48 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.200 Check model and map are aligned: 0.440 Set scattering table: 0.520 Process input model: 131.000 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.410 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: 0.020 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.002 0.032 76836 Z= 0.121 Angle : 0.482 10.254 104196 Z= 0.256 Chirality : 0.037 0.233 11376 Planarity : 0.003 0.051 13368 Dihedral : 13.750 87.235 28572 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.01 % Allowed : 0.50 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 9240 helix: 1.97 (0.07), residues: 5592 sheet: 0.23 (0.24), residues: 480 loop : -0.10 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 230 HIS 0.004 0.001 HIS C 530 PHE 0.006 0.001 PHE A 725 TYR 0.011 0.001 TYR C 576 ARG 0.006 0.000 ARG J 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1260 time to evaluate : 6.450 Fit side-chains REVERT: A 501 GLU cc_start: 0.6361 (pm20) cc_final: 0.6048 (mm-30) REVERT: A 544 SER cc_start: 0.8705 (p) cc_final: 0.8352 (t) REVERT: A 667 LYS cc_start: 0.8188 (tmmt) cc_final: 0.7740 (tmtt) REVERT: B 501 GLU cc_start: 0.6360 (pm20) cc_final: 0.6060 (mm-30) REVERT: B 544 SER cc_start: 0.8693 (p) cc_final: 0.8347 (t) REVERT: B 667 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7842 (tmtt) REVERT: C 28 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7403 (ptm160) REVERT: C 501 GLU cc_start: 0.7038 (pm20) cc_final: 0.6639 (mm-30) REVERT: D 28 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7429 (ptm160) REVERT: D 501 GLU cc_start: 0.6972 (pm20) cc_final: 0.6659 (mm-30) REVERT: E 501 GLU cc_start: 0.7155 (pm20) cc_final: 0.6559 (mm-30) REVERT: F 501 GLU cc_start: 0.6371 (pm20) cc_final: 0.6046 (mm-30) REVERT: F 544 SER cc_start: 0.8678 (p) cc_final: 0.8320 (t) REVERT: F 667 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7750 (tmtt) REVERT: H 501 GLU cc_start: 0.6380 (pm20) cc_final: 0.6065 (mm-30) REVERT: H 544 SER cc_start: 0.8655 (p) cc_final: 0.8302 (t) REVERT: H 667 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7785 (tmtt) REVERT: I 481 CYS cc_start: 0.7768 (m) cc_final: 0.7567 (m) REVERT: I 501 GLU cc_start: 0.7040 (pm20) cc_final: 0.6674 (mm-30) REVERT: J 28 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7496 (ptm160) REVERT: J 501 GLU cc_start: 0.7012 (pm20) cc_final: 0.6634 (mm-30) REVERT: K 501 GLU cc_start: 0.7154 (pm20) cc_final: 0.6547 (mm-30) REVERT: L 501 GLU cc_start: 0.7157 (pm20) cc_final: 0.6556 (mm-30) outliers start: 1 outliers final: 4 residues processed: 1260 average time/residue: 1.7880 time to fit residues: 2873.4067 Evaluate side-chains 774 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 770 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain H residue 385 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 780 optimal weight: 0.6980 chunk 700 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 472 optimal weight: 0.6980 chunk 374 optimal weight: 0.7980 chunk 724 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 440 optimal weight: 1.9990 chunk 539 optimal weight: 10.0000 chunk 839 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 384 HIS ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 384 HIS ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 GLN B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 40 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN D 37 GLN D 40 GLN ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 186 GLN E 384 HIS ** E 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 605 GLN F 40 GLN F 384 HIS ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 605 GLN F 710 ASN ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 186 GLN G 384 HIS ** G 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 40 GLN H 384 HIS ** H 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 605 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 605 GLN J 37 GLN J 40 GLN ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 40 GLN K 186 GLN K 384 HIS ** K 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 605 GLN L 37 GLN L 40 GLN L 186 GLN L 384 HIS ** L 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098802 restraints weight = 106410.601| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.86 r_work: 0.3094 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 76836 Z= 0.242 Angle : 0.558 8.953 104196 Z= 0.286 Chirality : 0.041 0.140 11376 Planarity : 0.004 0.038 13368 Dihedral : 3.961 26.822 10188 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.36 % Allowed : 8.11 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.09), residues: 9240 helix: 1.96 (0.07), residues: 5664 sheet: 0.17 (0.24), residues: 480 loop : -0.12 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 659 HIS 0.007 0.001 HIS C 384 PHE 0.017 0.002 PHE B 128 TYR 0.017 0.002 TYR L 637 ARG 0.014 0.000 ARG J 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 816 time to evaluate : 6.419 Fit side-chains REVERT: A 42 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7129 (ttm110) REVERT: A 82 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8351 (ptpp) REVERT: A 94 MET cc_start: 0.9022 (mmp) cc_final: 0.8803 (mmm) REVERT: A 186 GLN cc_start: 0.6932 (tp40) cc_final: 0.6731 (tp40) REVERT: A 187 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6987 (pt0) REVERT: A 202 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7208 (tpm170) REVERT: A 235 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6868 (mm-40) REVERT: A 286 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 638 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7064 (tp30) REVERT: A 678 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: B 42 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7190 (ttm110) REVERT: B 82 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8342 (ptpp) REVERT: B 94 MET cc_start: 0.9016 (mmp) cc_final: 0.8804 (mmm) REVERT: B 187 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: B 235 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6911 (mm-40) REVERT: B 286 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: B 385 MET cc_start: 0.7602 (mtm) cc_final: 0.6944 (ptp) REVERT: B 638 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: B 678 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8673 (mt-10) REVERT: C 28 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7917 (ptm160) REVERT: C 252 TYR cc_start: 0.5642 (m-80) cc_final: 0.5281 (m-80) REVERT: C 575 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7968 (ptm160) REVERT: C 632 LEU cc_start: 0.7905 (mt) cc_final: 0.7696 (mp) REVERT: D 28 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7924 (ptm160) REVERT: D 252 TYR cc_start: 0.5539 (m-80) cc_final: 0.5234 (m-80) REVERT: D 575 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7915 (ptm160) REVERT: D 632 LEU cc_start: 0.7956 (mt) cc_final: 0.7743 (mp) REVERT: E 46 ASP cc_start: 0.7974 (t0) cc_final: 0.7768 (t0) REVERT: E 50 LYS cc_start: 0.8969 (mttm) cc_final: 0.8758 (mtmt) REVERT: E 498 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8119 (t-90) REVERT: E 575 ARG cc_start: 0.7159 (mmt-90) cc_final: 0.6756 (mtp85) REVERT: E 638 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6560 (pp20) REVERT: F 42 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7114 (ttm110) REVERT: F 82 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8324 (ptpp) REVERT: F 94 MET cc_start: 0.9018 (mmp) cc_final: 0.8810 (mmm) REVERT: F 187 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: F 202 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7194 (tpm170) REVERT: F 235 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6861 (mm-40) REVERT: F 286 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: F 385 MET cc_start: 0.7565 (mtm) cc_final: 0.6870 (ptp) REVERT: F 638 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: F 678 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: G 498 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8121 (t-90) REVERT: G 501 GLU cc_start: 0.7683 (pm20) cc_final: 0.6766 (mm-30) REVERT: G 575 ARG cc_start: 0.7159 (mmt-90) cc_final: 0.6587 (mtp85) REVERT: G 638 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6594 (pp20) REVERT: H 42 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7117 (ttm110) REVERT: H 82 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: H 94 MET cc_start: 0.9024 (mmp) cc_final: 0.8815 (mmm) REVERT: H 187 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: H 202 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7209 (tpm170) REVERT: H 235 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6869 (mm-40) REVERT: H 286 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: H 385 MET cc_start: 0.7603 (mtm) cc_final: 0.6920 (ptp) REVERT: H 638 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: H 678 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: I 252 TYR cc_start: 0.5530 (m-80) cc_final: 0.5228 (m-80) REVERT: I 575 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7928 (ptm160) REVERT: I 756 ASP cc_start: 0.8180 (t0) cc_final: 0.7952 (m-30) REVERT: J 28 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7919 (ptm160) REVERT: J 252 TYR cc_start: 0.5510 (m-80) cc_final: 0.5193 (m-80) REVERT: J 575 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7916 (ptm160) REVERT: J 632 LEU cc_start: 0.7941 (mt) cc_final: 0.7711 (mp) REVERT: K 501 GLU cc_start: 0.7629 (pm20) cc_final: 0.6698 (mm-30) REVERT: K 575 ARG cc_start: 0.7173 (mmt-90) cc_final: 0.6607 (mtp85) REVERT: K 638 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6537 (pp20) REVERT: L 498 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: L 501 GLU cc_start: 0.7639 (pm20) cc_final: 0.6701 (mm-30) REVERT: L 575 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6592 (mtp85) REVERT: L 638 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6524 (pp20) outliers start: 190 outliers final: 54 residues processed: 926 average time/residue: 1.7450 time to fit residues: 2077.7992 Evaluate side-chains 781 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 697 time to evaluate : 6.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 638 GLU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 678 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 638 GLU Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 678 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 271 CYS Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 271 CYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 638 GLU Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 266 GLN Chi-restraints excluded: chain L residue 283 ASN Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 498 HIS Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 638 GLU Chi-restraints excluded: chain L residue 785 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 352 optimal weight: 5.9990 chunk 738 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 443 optimal weight: 0.9980 chunk 375 optimal weight: 2.9990 chunk 446 optimal weight: 9.9990 chunk 698 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 916 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS A 710 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN C 308 GLN C 384 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 308 GLN ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 GLN D 668 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 474 HIS ** E 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 HIS ** F 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN G 474 HIS ** G 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 HIS H 710 ASN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN I 308 GLN ** I 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 668 GLN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN J 308 GLN ** J 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 605 GLN J 668 GLN ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN K 474 HIS ** K 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 GLN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 474 HIS ** L 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 668 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094623 restraints weight = 105150.083| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 76836 Z= 0.378 Angle : 0.611 9.856 104196 Z= 0.313 Chirality : 0.043 0.147 11376 Planarity : 0.004 0.038 13368 Dihedral : 4.239 21.773 10176 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.70 % Allowed : 9.39 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 9240 helix: 1.70 (0.07), residues: 5652 sheet: -0.12 (0.23), residues: 480 loop : -0.40 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 659 HIS 0.008 0.001 HIS C 384 PHE 0.020 0.002 PHE F 495 TYR 0.017 0.002 TYR C 13 ARG 0.009 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 765 time to evaluate : 6.654 Fit side-chains REVERT: A 42 ARG cc_start: 0.7334 (ttm110) cc_final: 0.7073 (ttm110) REVERT: A 82 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (ptpp) REVERT: A 186 GLN cc_start: 0.6868 (tp40) cc_final: 0.6642 (tp40) REVERT: A 187 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6935 (pt0) REVERT: A 502 ASP cc_start: 0.7972 (p0) cc_final: 0.7658 (p0) REVERT: A 638 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: A 756 ASP cc_start: 0.8256 (t0) cc_final: 0.7958 (t70) REVERT: B 42 ARG cc_start: 0.7344 (ttm110) cc_final: 0.6861 (ttm170) REVERT: B 82 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8493 (ptpp) REVERT: B 187 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6939 (pt0) REVERT: B 306 LEU cc_start: 0.8581 (tp) cc_final: 0.8331 (tt) REVERT: B 502 ASP cc_start: 0.7911 (p0) cc_final: 0.7576 (p0) REVERT: B 638 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: B 756 ASP cc_start: 0.8241 (t0) cc_final: 0.7941 (t70) REVERT: C 252 TYR cc_start: 0.5671 (m-80) cc_final: 0.5240 (m-80) REVERT: C 575 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8035 (ptm160) REVERT: D 252 TYR cc_start: 0.5674 (m-80) cc_final: 0.5240 (m-80) REVERT: D 575 ARG cc_start: 0.8230 (ttm110) cc_final: 0.8020 (ptm160) REVERT: E 42 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6610 (ttm110) REVERT: E 46 ASP cc_start: 0.7919 (t0) cc_final: 0.7692 (t0) REVERT: E 305 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8631 (tm) REVERT: F 42 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7096 (ttm110) REVERT: F 82 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8549 (ptpp) REVERT: F 187 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: F 502 ASP cc_start: 0.7910 (p0) cc_final: 0.7582 (p0) REVERT: F 638 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: F 756 ASP cc_start: 0.8237 (t0) cc_final: 0.7949 (t70) REVERT: G 42 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6667 (ttm110) REVERT: G 305 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8634 (tm) REVERT: H 42 ARG cc_start: 0.7350 (ttm110) cc_final: 0.6878 (ttm170) REVERT: H 82 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8553 (ptpp) REVERT: H 187 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: H 306 LEU cc_start: 0.8568 (tp) cc_final: 0.8302 (tt) REVERT: H 502 ASP cc_start: 0.7907 (p0) cc_final: 0.7593 (p0) REVERT: H 638 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7085 (tp30) REVERT: H 756 ASP cc_start: 0.8234 (t0) cc_final: 0.7938 (t70) REVERT: I 252 TYR cc_start: 0.5718 (m-80) cc_final: 0.5215 (m-80) REVERT: I 286 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: J 252 TYR cc_start: 0.5660 (m-80) cc_final: 0.5175 (m-80) REVERT: K 42 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: K 305 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8611 (tm) REVERT: L 42 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6651 (ttm110) REVERT: L 305 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8614 (tm) REVERT: L 385 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7287 (mtp) outliers start: 217 outliers final: 78 residues processed: 896 average time/residue: 1.6950 time to fit residues: 1964.8630 Evaluate side-chains 770 residues out of total 8208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 670 time to evaluate : 6.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 638 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 498 HIS Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 266 GLN Chi-restraints excluded: chain L residue 283 ASN Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 498 HIS Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 642 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5701 > 50: distance: 66 - 122: 21.880 distance: 69 - 119: 17.851 distance: 82 - 102: 24.894 distance: 85 - 99: 20.278 distance: 97 - 99: 21.660 distance: 99 - 100: 16.839 distance: 100 - 103: 7.506 distance: 101 - 102: 21.846 distance: 101 - 110: 17.047 distance: 103 - 104: 18.529 distance: 104 - 105: 17.384 distance: 105 - 106: 13.481 distance: 106 - 107: 17.382 distance: 107 - 108: 15.352 distance: 107 - 109: 14.294 distance: 110 - 111: 19.211 distance: 111 - 112: 10.326 distance: 111 - 114: 7.183 distance: 112 - 113: 28.307 distance: 112 - 119: 16.456 distance: 114 - 115: 9.977 distance: 115 - 116: 10.401 distance: 116 - 117: 5.514 distance: 116 - 118: 11.647 distance: 119 - 120: 18.073 distance: 120 - 121: 13.748 distance: 120 - 123: 26.651 distance: 121 - 122: 35.855 distance: 121 - 131: 25.747 distance: 123 - 124: 11.768 distance: 124 - 125: 20.109 distance: 124 - 126: 19.443 distance: 125 - 127: 25.372 distance: 126 - 128: 26.192 distance: 127 - 129: 10.397 distance: 128 - 129: 33.163 distance: 129 - 130: 18.407 distance: 131 - 132: 12.494 distance: 132 - 133: 43.538 distance: 133 - 135: 21.190 distance: 135 - 136: 32.513 distance: 136 - 137: 8.162 distance: 136 - 139: 13.151 distance: 137 - 138: 13.032 distance: 137 - 146: 25.653 distance: 139 - 140: 23.786 distance: 140 - 141: 18.824 distance: 140 - 142: 12.669 distance: 141 - 143: 16.630 distance: 142 - 144: 24.494 distance: 143 - 145: 33.289 distance: 144 - 145: 22.659 distance: 146 - 147: 14.856 distance: 147 - 148: 21.788 distance: 147 - 150: 24.490 distance: 148 - 149: 8.114 distance: 148 - 151: 35.427 distance: 151 - 152: 15.505 distance: 152 - 153: 27.907 distance: 152 - 155: 25.537 distance: 153 - 154: 22.470 distance: 153 - 158: 20.098 distance: 155 - 156: 26.348 distance: 155 - 157: 24.709 distance: 158 - 159: 12.980 distance: 159 - 160: 36.032 distance: 159 - 162: 8.983 distance: 160 - 161: 12.701 distance: 160 - 165: 26.376 distance: 162 - 163: 26.947 distance: 162 - 164: 34.105 distance: 165 - 166: 12.168 distance: 166 - 167: 18.008 distance: 166 - 169: 40.599 distance: 167 - 168: 11.700 distance: 167 - 179: 15.034 distance: 169 - 170: 11.386 distance: 170 - 171: 14.420 distance: 170 - 172: 14.067 distance: 171 - 173: 4.027 distance: 172 - 174: 9.320 distance: 172 - 175: 8.176 distance: 173 - 174: 4.282 distance: 174 - 176: 8.177 distance: 175 - 177: 6.473 distance: 176 - 178: 6.893 distance: 177 - 178: 9.513 distance: 179 - 180: 4.881 distance: 179 - 185: 12.212 distance: 180 - 181: 9.000 distance: 180 - 183: 8.467 distance: 181 - 182: 9.150 distance: 181 - 186: 6.467 distance: 183 - 184: 20.251 distance: 184 - 185: 6.051