Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 01:20:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/10_2023/3j6q_5926_updated.pdb" } resolution = 3.8 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= 1.202 sd= 10.389 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 235 5.16 5 C 26930 2.51 5 N 7375 2.21 5 O 8030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 543": "OE1" <-> "OE2" Residue "D TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1023": "OE1" <-> "OE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 543": "OE1" <-> "OE2" Residue "E TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1023": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 42575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 20.82, per 1000 atoms: 0.49 Number of scatterers: 42575 At special positions: 0 Unit cell: (179.4, 177.008, 111.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 235 16.00 P 5 15.00 O 8030 8.00 N 7375 7.00 C 26930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.83 Conformation dependent library (CDL) restraints added in 6.3 seconds 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 40 sheets defined 26.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.51 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 77' Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.763A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.602A pdb=" N THR A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.416A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 removed outlier: 3.778A pdb=" N LEU A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.709A pdb=" N ASN A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.901A pdb=" N ALA A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.812A pdb=" N GLU A 243 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.563A pdb=" N ILE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.521A pdb=" N ASP A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 330 through 340 removed outlier: 3.577A pdb=" N LEU A 335 " --> pdb=" O HIS A 332 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 340 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.679A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.634A pdb=" N PHE A 456 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 457' Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.833A pdb=" N LEU A 466 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A 467 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Proline residue: A 468 - end of helix Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 496 Processing helix chain 'A' and resid 527 through 543 removed outlier: 4.352A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 574 No H-bonds generated for 'chain 'A' and resid 571 through 574' Processing helix chain 'A' and resid 625 through 636 removed outlier: 4.246A pdb=" N SER A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 removed outlier: 3.575A pdb=" N ASN A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 713 No H-bonds generated for 'chain 'A' and resid 710 through 713' Processing helix chain 'A' and resid 752 through 759 Proline residue: A 756 - end of helix removed outlier: 3.622A pdb=" N LEU A 759 " --> pdb=" O PRO A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.623A pdb=" N ALA A 793 " --> pdb=" O PRO A 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 808 No H-bonds generated for 'chain 'A' and resid 805 through 808' Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.699A pdb=" N ILE A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 941 through 950 removed outlier: 4.436A pdb=" N VAL A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 1000 through 1007 removed outlier: 3.682A pdb=" N LEU A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1040 through 1046 removed outlier: 4.197A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 65 through 68 No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.762A pdb=" N ILE B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.600A pdb=" N THR B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 removed outlier: 4.415A pdb=" N VAL B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 removed outlier: 3.779A pdb=" N LEU B 141 " --> pdb=" O PRO B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.709A pdb=" N ASN B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.901A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.811A pdb=" N GLU B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 removed outlier: 3.563A pdb=" N ILE B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.519A pdb=" N ASP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.578A pdb=" N LEU B 335 " --> pdb=" O HIS B 332 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 340 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.678A pdb=" N ASP B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.634A pdb=" N PHE B 456 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 457' Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.835A pdb=" N LEU B 466 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER B 467 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 527 through 543 removed outlier: 4.352A pdb=" N LYS B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 574 No H-bonds generated for 'chain 'B' and resid 571 through 574' Processing helix chain 'B' and resid 625 through 636 removed outlier: 4.247A pdb=" N SER B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 666 removed outlier: 3.575A pdb=" N ASN B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 713 No H-bonds generated for 'chain 'B' and resid 710 through 713' Processing helix chain 'B' and resid 752 through 759 Proline residue: B 756 - end of helix removed outlier: 3.620A pdb=" N LEU B 759 " --> pdb=" O PRO B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'B' and resid 789 through 795 removed outlier: 3.624A pdb=" N ALA B 793 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 808 No H-bonds generated for 'chain 'B' and resid 805 through 808' Processing helix chain 'B' and resid 834 through 849 removed outlier: 3.951A pdb=" N LYS B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 848 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 892 No H-bonds generated for 'chain 'B' and resid 889 through 892' Processing helix chain 'B' and resid 941 through 950 removed outlier: 4.436A pdb=" N VAL B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 970 No H-bonds generated for 'chain 'B' and resid 967 through 970' Processing helix chain 'B' and resid 1000 through 1007 removed outlier: 3.681A pdb=" N LEU B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1031 Processing helix chain 'B' and resid 1040 through 1046 removed outlier: 4.199A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 77' Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.763A pdb=" N ILE C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.601A pdb=" N THR C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 4.416A pdb=" N VAL C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 141 removed outlier: 3.777A pdb=" N LEU C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.709A pdb=" N ASN C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 228 through 235 removed outlier: 3.901A pdb=" N ALA C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.812A pdb=" N GLU C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 276 removed outlier: 3.565A pdb=" N ILE C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.520A pdb=" N ASP C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.577A pdb=" N LEU C 335 " --> pdb=" O HIS C 332 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 338 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 340 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 436 through 446 removed outlier: 3.678A pdb=" N ASP C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 removed outlier: 3.633A pdb=" N PHE C 456 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 457 " --> pdb=" O GLY C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 457' Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.833A pdb=" N LEU C 466 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER C 467 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Proline residue: C 468 - end of helix Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 496 Processing helix chain 'C' and resid 527 through 543 removed outlier: 4.352A pdb=" N LYS C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 574 No H-bonds generated for 'chain 'C' and resid 571 through 574' Processing helix chain 'C' and resid 625 through 636 removed outlier: 4.245A pdb=" N SER C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 634 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 666 removed outlier: 3.575A pdb=" N ASN C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 713 No H-bonds generated for 'chain 'C' and resid 710 through 713' Processing helix chain 'C' and resid 752 through 759 Proline residue: C 756 - end of helix removed outlier: 3.620A pdb=" N LEU C 759 " --> pdb=" O PRO C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 764 No H-bonds generated for 'chain 'C' and resid 762 through 764' Processing helix chain 'C' and resid 789 through 795 removed outlier: 3.622A pdb=" N ALA C 793 " --> pdb=" O PRO C 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 808 No H-bonds generated for 'chain 'C' and resid 805 through 808' Processing helix chain 'C' and resid 834 through 849 removed outlier: 3.952A pdb=" N LYS C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 847 " --> pdb=" O ALA C 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 892 No H-bonds generated for 'chain 'C' and resid 889 through 892' Processing helix chain 'C' and resid 941 through 950 removed outlier: 4.436A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 970 No H-bonds generated for 'chain 'C' and resid 967 through 970' Processing helix chain 'C' and resid 1000 through 1007 removed outlier: 3.682A pdb=" N LEU C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1031 Processing helix chain 'C' and resid 1040 through 1046 removed outlier: 4.199A pdb=" N VAL C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 65 through 68 No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.762A pdb=" N ILE D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.601A pdb=" N THR D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 removed outlier: 4.416A pdb=" N VAL D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 141 removed outlier: 3.779A pdb=" N LEU D 141 " --> pdb=" O PRO D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 189 through 195 removed outlier: 3.708A pdb=" N ASN D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 228 through 235 removed outlier: 3.900A pdb=" N ALA D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.812A pdb=" N GLU D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 removed outlier: 3.565A pdb=" N ILE D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 removed outlier: 3.520A pdb=" N ASP D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.576A pdb=" N LEU D 335 " --> pdb=" O HIS D 332 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 338 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 340 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 436 through 446 removed outlier: 3.678A pdb=" N ASP D 446 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 removed outlier: 3.634A pdb=" N PHE D 456 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 457 " --> pdb=" O GLY D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 457' Processing helix chain 'D' and resid 462 through 470 removed outlier: 3.834A pdb=" N LEU D 466 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER D 467 " --> pdb=" O ASP D 464 " (cutoff:3.500A) Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 473 through 477 Processing helix chain 'D' and resid 491 through 496 Processing helix chain 'D' and resid 527 through 543 removed outlier: 4.354A pdb=" N LYS D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 537 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 574 No H-bonds generated for 'chain 'D' and resid 571 through 574' Processing helix chain 'D' and resid 625 through 636 removed outlier: 4.245A pdb=" N SER D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 634 " --> pdb=" O SER D 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 666 removed outlier: 3.575A pdb=" N ASN D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 713 No H-bonds generated for 'chain 'D' and resid 710 through 713' Processing helix chain 'D' and resid 752 through 759 Proline residue: D 756 - end of helix removed outlier: 3.622A pdb=" N LEU D 759 " --> pdb=" O PRO D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 764 No H-bonds generated for 'chain 'D' and resid 762 through 764' Processing helix chain 'D' and resid 789 through 795 removed outlier: 3.622A pdb=" N ALA D 793 " --> pdb=" O PRO D 789 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 808 No H-bonds generated for 'chain 'D' and resid 805 through 808' Processing helix chain 'D' and resid 834 through 849 removed outlier: 3.951A pdb=" N LYS D 838 " --> pdb=" O THR D 834 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 845 " --> pdb=" O MET D 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 847 " --> pdb=" O ALA D 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 848 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 892 No H-bonds generated for 'chain 'D' and resid 889 through 892' Processing helix chain 'D' and resid 941 through 950 removed outlier: 4.438A pdb=" N VAL D 946 " --> pdb=" O LYS D 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 949 " --> pdb=" O ASN D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 970 No H-bonds generated for 'chain 'D' and resid 967 through 970' Processing helix chain 'D' and resid 1000 through 1007 removed outlier: 3.681A pdb=" N LEU D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU D1007 " --> pdb=" O VAL D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1031 Processing helix chain 'D' and resid 1040 through 1046 removed outlier: 4.199A pdb=" N VAL D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 65 through 68 No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 77' Processing helix chain 'E' and resid 85 through 97 removed outlier: 3.763A pdb=" N ILE E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.600A pdb=" N THR E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 removed outlier: 4.416A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.779A pdb=" N LEU E 141 " --> pdb=" O PRO E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 189 through 195 removed outlier: 3.709A pdb=" N ASN E 193 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 228 through 235 removed outlier: 3.900A pdb=" N ALA E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.812A pdb=" N GLU E 243 " --> pdb=" O TRP E 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS E 247 " --> pdb=" O GLU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 276 removed outlier: 3.564A pdb=" N ILE E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.520A pdb=" N ASP E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 303 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 320 Processing helix chain 'E' and resid 330 through 340 removed outlier: 3.578A pdb=" N LEU E 335 " --> pdb=" O HIS E 332 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 338 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 340 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.679A pdb=" N ASP E 446 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 457 removed outlier: 3.635A pdb=" N PHE E 456 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN E 457 " --> pdb=" O GLY E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 453 through 457' Processing helix chain 'E' and resid 462 through 470 removed outlier: 3.833A pdb=" N LEU E 466 " --> pdb=" O ASP E 463 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER E 467 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Proline residue: E 468 - end of helix Processing helix chain 'E' and resid 473 through 477 Processing helix chain 'E' and resid 491 through 496 Processing helix chain 'E' and resid 527 through 543 removed outlier: 4.353A pdb=" N LYS E 531 " --> pdb=" O ASN E 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET E 532 " --> pdb=" O SER E 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 543 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 574 No H-bonds generated for 'chain 'E' and resid 571 through 574' Processing helix chain 'E' and resid 625 through 636 removed outlier: 4.246A pdb=" N SER E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 631 " --> pdb=" O SER E 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 634 " --> pdb=" O SER E 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 636 " --> pdb=" O THR E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 666 removed outlier: 3.575A pdb=" N ASN E 659 " --> pdb=" O GLU E 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 665 " --> pdb=" O VAL E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 713 No H-bonds generated for 'chain 'E' and resid 710 through 713' Processing helix chain 'E' and resid 752 through 759 Proline residue: E 756 - end of helix removed outlier: 3.620A pdb=" N LEU E 759 " --> pdb=" O PRO E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 764 No H-bonds generated for 'chain 'E' and resid 762 through 764' Processing helix chain 'E' and resid 789 through 795 removed outlier: 3.622A pdb=" N ALA E 793 " --> pdb=" O PRO E 789 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 794 " --> pdb=" O ALA E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 808 No H-bonds generated for 'chain 'E' and resid 805 through 808' Processing helix chain 'E' and resid 834 through 849 removed outlier: 3.950A pdb=" N LYS E 838 " --> pdb=" O THR E 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 845 " --> pdb=" O MET E 841 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 848 " --> pdb=" O LEU E 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 892 No H-bonds generated for 'chain 'E' and resid 889 through 892' Processing helix chain 'E' and resid 941 through 950 removed outlier: 4.437A pdb=" N VAL E 946 " --> pdb=" O LYS E 942 " (cutoff:3.500A) Processing helix chain 'E' and resid 967 through 970 No H-bonds generated for 'chain 'E' and resid 967 through 970' Processing helix chain 'E' and resid 1000 through 1007 removed outlier: 3.682A pdb=" N LEU E1005 " --> pdb=" O ALA E1001 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E1007 " --> pdb=" O VAL E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1031 Processing helix chain 'E' and resid 1040 through 1046 removed outlier: 4.198A pdb=" N VAL E1045 " --> pdb=" O ALA E1041 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= C, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= D, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.957A pdb=" N ILE A 373 " --> pdb=" O THR A 771 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 771 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 768 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 786 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.724A pdb=" N THR A 823 " --> pdb=" O THR A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 419 through 421 Processing sheet with id= G, first strand: chain 'A' and resid 582 through 587 removed outlier: 6.641A pdb=" N THR A 556 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 585 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 558 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET A 587 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 560 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 612 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 561 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 614 " --> pdb=" O LEU A 561 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 1015 through 1017 removed outlier: 3.665A pdb=" N VAL A1052 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 959 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 919 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 961 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE A 921 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN A 857 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU A 920 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 859 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS A 877 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER A 860 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 879 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR B 41 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 50 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 43 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= K, first strand: chain 'B' and resid 326 through 328 Processing sheet with id= L, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.956A pdb=" N ILE B 373 " --> pdb=" O THR B 771 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 771 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.723A pdb=" N THR B 823 " --> pdb=" O THR B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 419 through 421 Processing sheet with id= O, first strand: chain 'B' and resid 582 through 587 removed outlier: 6.640A pdb=" N THR B 556 " --> pdb=" O ARG B 583 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE B 585 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 558 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET B 587 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 560 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE B 612 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU B 561 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 614 " --> pdb=" O LEU B 561 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 1015 through 1017 removed outlier: 3.666A pdb=" N VAL B1052 " --> pdb=" O ILE B1017 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR B 959 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B 919 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER B 961 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 921 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLN B 857 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU B 920 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 859 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS B 877 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER B 860 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 879 " --> pdb=" O SER B 860 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR C 41 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 50 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 43 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= S, first strand: chain 'C' and resid 326 through 328 Processing sheet with id= T, first strand: chain 'C' and resid 373 through 376 removed outlier: 3.957A pdb=" N ILE C 373 " --> pdb=" O THR C 771 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 771 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C 768 " --> pdb=" O ARG C 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 786 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 401 through 403 removed outlier: 6.722A pdb=" N THR C 823 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 419 through 421 Processing sheet with id= W, first strand: chain 'C' and resid 582 through 587 removed outlier: 6.641A pdb=" N THR C 556 " --> pdb=" O ARG C 583 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE C 585 " --> pdb=" O THR C 556 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 558 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 587 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU C 560 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE C 612 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 561 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 614 " --> pdb=" O LEU C 561 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 1015 through 1017 removed outlier: 3.667A pdb=" N VAL C1052 " --> pdb=" O ILE C1017 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR C 959 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 919 " --> pdb=" O TYR C 959 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER C 961 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 921 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLN C 857 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU C 920 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 859 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS C 877 " --> pdb=" O VAL C 858 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER C 860 " --> pdb=" O LYS C 877 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 879 " --> pdb=" O SER C 860 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 50 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 43 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 161 through 165 Processing sheet with id= AA, first strand: chain 'D' and resid 326 through 328 Processing sheet with id= AB, first strand: chain 'D' and resid 373 through 376 removed outlier: 3.956A pdb=" N ILE D 373 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 771 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU D 768 " --> pdb=" O ARG D 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG D 786 " --> pdb=" O GLU D 768 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 401 through 403 removed outlier: 6.724A pdb=" N THR D 823 " --> pdb=" O THR D 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'D' and resid 419 through 421 Processing sheet with id= AE, first strand: chain 'D' and resid 582 through 587 removed outlier: 6.640A pdb=" N THR D 556 " --> pdb=" O ARG D 583 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 585 " --> pdb=" O THR D 556 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 558 " --> pdb=" O ILE D 585 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET D 587 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 560 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 612 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU D 561 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 614 " --> pdb=" O LEU D 561 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'D' and resid 1015 through 1017 removed outlier: 3.666A pdb=" N VAL D1052 " --> pdb=" O ILE D1017 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR D 959 " --> pdb=" O SER D 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR D 919 " --> pdb=" O TYR D 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER D 961 " --> pdb=" O TYR D 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE D 921 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN D 857 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU D 920 " --> pdb=" O GLN D 857 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 859 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS D 877 " --> pdb=" O VAL D 858 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER D 860 " --> pdb=" O LYS D 877 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 879 " --> pdb=" O SER D 860 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 39 through 43 removed outlier: 3.713A pdb=" N THR E 41 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 50 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN E 43 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 161 through 165 Processing sheet with id= AI, first strand: chain 'E' and resid 326 through 328 Processing sheet with id= AJ, first strand: chain 'E' and resid 373 through 376 removed outlier: 3.956A pdb=" N ILE E 373 " --> pdb=" O THR E 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 771 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU E 768 " --> pdb=" O ARG E 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG E 786 " --> pdb=" O GLU E 768 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 401 through 403 removed outlier: 6.723A pdb=" N THR E 823 " --> pdb=" O THR E 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'E' and resid 419 through 421 Processing sheet with id= AM, first strand: chain 'E' and resid 582 through 587 removed outlier: 6.640A pdb=" N THR E 556 " --> pdb=" O ARG E 583 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE E 585 " --> pdb=" O THR E 556 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 558 " --> pdb=" O ILE E 585 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET E 587 " --> pdb=" O ILE E 558 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 560 " --> pdb=" O MET E 587 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE E 612 " --> pdb=" O ILE E 559 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU E 561 " --> pdb=" O PHE E 612 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 614 " --> pdb=" O LEU E 561 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'E' and resid 1015 through 1017 removed outlier: 3.666A pdb=" N VAL E1052 " --> pdb=" O ILE E1017 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR E 959 " --> pdb=" O SER E 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR E 919 " --> pdb=" O TYR E 959 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER E 961 " --> pdb=" O TYR E 919 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 921 " --> pdb=" O SER E 961 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLN E 857 " --> pdb=" O ILE E 918 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU E 920 " --> pdb=" O GLN E 857 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL E 859 " --> pdb=" O LEU E 920 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS E 877 " --> pdb=" O VAL E 858 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER E 860 " --> pdb=" O LYS E 877 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 879 " --> pdb=" O SER E 860 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1821 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: 15.34 Time building geometry restraints manager: 17.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8207 1.33 - 1.45: 10538 1.45 - 1.57: 24345 1.57 - 1.69: 10 1.69 - 1.81: 435 Bond restraints: 43535 Sorted by residual: bond pdb=" NZ GPL C 234 " pdb=" P GPL C 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" NZ GPL A 234 " pdb=" P GPL A 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" NZ GPL E 234 " pdb=" P GPL E 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" NZ GPL B 234 " pdb=" P GPL B 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" NZ GPL D 234 " pdb=" P GPL D 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.18e+01 ... (remaining 43530 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.08: 1584 107.08 - 114.41: 25288 114.41 - 121.74: 23116 121.74 - 129.07: 9057 129.07 - 136.39: 285 Bond angle restraints: 59330 Sorted by residual: angle pdb=" N CYS D 639 " pdb=" CA CYS D 639 " pdb=" CB CYS D 639 " ideal model delta sigma weight residual 110.90 102.66 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" N CYS E 639 " pdb=" CA CYS E 639 " pdb=" CB CYS E 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS B 639 " pdb=" CA CYS B 639 " pdb=" CB CYS B 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS A 639 " pdb=" CA CYS A 639 " pdb=" CB CYS A 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.77e+01 angle pdb=" N CYS C 639 " pdb=" CA CYS C 639 " pdb=" CB CYS C 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.76e+01 ... (remaining 59325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 25300 20.44 - 40.89: 710 40.89 - 61.33: 150 61.33 - 81.77: 20 81.77 - 102.21: 5 Dihedral angle restraints: 26185 sinusoidal: 10430 harmonic: 15755 Sorted by residual: dihedral pdb=" CA ALA E 308 " pdb=" C ALA E 308 " pdb=" N ASN E 309 " pdb=" CA ASN E 309 " ideal model delta harmonic sigma weight residual -180.00 -77.79 -102.21 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA A 308 " pdb=" C ALA A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta harmonic sigma weight residual -180.00 -77.80 -102.20 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA C 308 " pdb=" C ALA C 308 " pdb=" N ASN C 309 " pdb=" CA ASN C 309 " ideal model delta harmonic sigma weight residual -180.00 -77.92 -102.08 0 5.00e+00 4.00e-02 4.17e+02 ... (remaining 26182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4629 0.061 - 0.122: 1844 0.122 - 0.183: 333 0.183 - 0.243: 45 0.243 - 0.304: 4 Chirality restraints: 6855 Sorted by residual: chirality pdb=" P GPL E 234 " pdb=" NZ GPL E 234 " pdb=" O2P GPL E 234 " pdb=" O5' GPL E 234 " both_signs ideal model delta sigma weight residual True 3.19 3.50 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P GPL D 234 " pdb=" NZ GPL D 234 " pdb=" O2P GPL D 234 " pdb=" O5' GPL D 234 " both_signs ideal model delta sigma weight residual True 3.19 3.50 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" P GPL C 234 " pdb=" NZ GPL C 234 " pdb=" O2P GPL C 234 " pdb=" O5' GPL C 234 " both_signs ideal model delta sigma weight residual True 3.19 3.49 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 6852 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" CG ASP C 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP C 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP C 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" CG ASP E 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP E 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 481 " -0.012 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CG ASP B 481 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP B 481 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 481 " -0.016 2.00e-02 2.50e+03 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 30 2.00 - 2.73: 3432 2.73 - 3.45: 57845 3.45 - 4.18: 94951 4.18 - 4.90: 162375 Nonbonded interactions: 318633 Sorted by model distance: nonbonded pdb=" CB PRO A 601 " pdb=" NH2 ARG B 886 " model vdw 1.279 3.520 nonbonded pdb=" CB PRO C 601 " pdb=" NH2 ARG D 886 " model vdw 1.279 3.520 nonbonded pdb=" NH2 ARG A 886 " pdb=" CB PRO E 601 " model vdw 1.281 3.520 nonbonded pdb=" CB PRO D 601 " pdb=" NH2 ARG E 886 " model vdw 1.302 3.520 nonbonded pdb=" CB PRO B 601 " pdb=" NH2 ARG C 886 " model vdw 1.306 3.520 ... (remaining 318628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.530 Check model and map are aligned: 0.700 Set scattering table: 0.400 Process input model: 100.960 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 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 : 0.010 0.182 43535 Z= 0.676 Angle : 1.163 13.000 59330 Z= 0.773 Chirality : 0.055 0.304 6855 Planarity : 0.008 0.047 7560 Dihedral : 10.655 102.215 15985 Min Nonbonded Distance : 1.279 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 4.20 % Allowed : 11.68 % Favored : 84.12 % Rotamer: Outliers : 0.64 % Allowed : 1.70 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.09), residues: 5265 helix: -3.64 (0.08), residues: 1480 sheet: -1.00 (0.17), residues: 730 loop : -3.43 (0.10), residues: 3055 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1438 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 3 residues processed: 1463 average time/residue: 0.5976 time to fit residues: 1388.8627 Evaluate side-chains 664 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 661 time to evaluate : 4.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4513 time to fit residues: 8.9866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 443 optimal weight: 4.9990 chunk 397 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 411 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 476 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 21 GLN ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 281 ASN A 385 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 8 ASN B 33 GLN B 49 HIS B 385 HIS B 544 ASN B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN C 8 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 623 GLN C 683 GLN D 8 ASN D 21 GLN D 33 GLN D 281 ASN ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 GLN D 973 GLN E 8 ASN E 241 GLN E 270 GLN E 281 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 GLN E 806 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43535 Z= 0.220 Angle : 0.771 9.403 59330 Z= 0.394 Chirality : 0.047 0.246 6855 Planarity : 0.006 0.080 7560 Dihedral : 6.873 71.323 5950 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 1.12 % Allowed : 11.43 % Favored : 87.45 % Rotamer: Outliers : 3.57 % Allowed : 10.89 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.10), residues: 5265 helix: -2.56 (0.11), residues: 1340 sheet: -0.58 (0.18), residues: 795 loop : -3.06 (0.10), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 753 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 97 residues processed: 884 average time/residue: 0.5255 time to fit residues: 768.5378 Evaluate side-chains 643 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 546 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.3846 time to fit residues: 78.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 264 optimal weight: 40.0000 chunk 147 optimal weight: 30.0000 chunk 396 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 477 optimal weight: 6.9990 chunk 515 optimal weight: 6.9990 chunk 425 optimal weight: 7.9990 chunk 473 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 383 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 33 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 212 HIS D 385 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 848 GLN D1048 HIS E 33 GLN E 49 HIS E 93 HIS E 212 HIS E 385 HIS ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 43535 Z= 0.273 Angle : 0.740 9.460 59330 Z= 0.381 Chirality : 0.047 0.203 6855 Planarity : 0.006 0.095 7560 Dihedral : 6.369 60.608 5950 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.80 % Allowed : 12.35 % Favored : 86.86 % Rotamer: Outliers : 2.65 % Allowed : 12.95 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5265 helix: -2.16 (0.12), residues: 1485 sheet: -0.35 (0.20), residues: 735 loop : -2.90 (0.10), residues: 3045 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 567 time to evaluate : 4.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 69 residues processed: 663 average time/residue: 0.5382 time to fit residues: 604.1427 Evaluate side-chains 549 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 480 time to evaluate : 4.781 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.3995 time to fit residues: 58.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 0.0270 chunk 359 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 chunk 479 optimal weight: 4.9990 chunk 507 optimal weight: 30.0000 chunk 250 optimal weight: 6.9990 chunk 454 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43535 Z= 0.194 Angle : 0.680 11.902 59330 Z= 0.346 Chirality : 0.045 0.232 6855 Planarity : 0.005 0.072 7560 Dihedral : 6.078 58.011 5950 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.52 % Favored : 88.81 % Rotamer: Outliers : 1.93 % Allowed : 14.48 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 5265 helix: -1.87 (0.12), residues: 1480 sheet: -0.25 (0.20), residues: 750 loop : -2.80 (0.10), residues: 3035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 513 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 54 residues processed: 577 average time/residue: 0.5324 time to fit residues: 533.2220 Evaluate side-chains 522 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 468 time to evaluate : 4.825 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4067 time to fit residues: 46.9837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 422 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 377 optimal weight: 6.9990 chunk 209 optimal weight: 30.0000 chunk 433 optimal weight: 6.9990 chunk 350 optimal weight: 0.0980 chunk 0 optimal weight: 50.0000 chunk 259 optimal weight: 7.9990 chunk 455 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 434 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN D 375 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43535 Z= 0.199 Angle : 0.671 11.074 59330 Z= 0.341 Chirality : 0.045 0.269 6855 Planarity : 0.005 0.068 7560 Dihedral : 5.986 59.337 5950 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.90 % Favored : 88.45 % Rotamer: Outliers : 1.34 % Allowed : 15.94 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.94 (0.11), residues: 5265 helix: -1.63 (0.12), residues: 1505 sheet: -0.27 (0.19), residues: 765 loop : -2.69 (0.11), residues: 2995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 520 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 24 residues processed: 554 average time/residue: 0.5063 time to fit residues: 477.4590 Evaluate side-chains 484 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 460 time to evaluate : 4.613 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3880 time to fit residues: 23.8003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 30.0000 chunk 456 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 297 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 507 optimal weight: 30.0000 chunk 421 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 168 optimal weight: 40.0000 chunk 266 optimal weight: 20.0000 overall best weight: 9.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 212 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN A1048 HIS B 21 GLN B 492 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 21 GLN C 33 GLN C 61 ASN C 93 HIS ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN C 905 GLN C 916 ASN C1048 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 ASN D 651 ASN D 753 GLN E 61 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 779 ASN E1048 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43535 Z= 0.306 Angle : 0.764 12.617 59330 Z= 0.388 Chirality : 0.048 0.176 6855 Planarity : 0.006 0.070 7560 Dihedral : 6.354 59.350 5950 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.15 % Favored : 88.17 % Rotamer: Outliers : 2.27 % Allowed : 16.31 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 5265 helix: -1.70 (0.12), residues: 1545 sheet: -0.35 (0.19), residues: 700 loop : -2.84 (0.10), residues: 3020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 484 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 58 residues processed: 562 average time/residue: 0.4931 time to fit residues: 472.5065 Evaluate side-chains 486 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 428 time to evaluate : 4.901 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3976 time to fit residues: 49.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 489 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 289 optimal weight: 30.0000 chunk 370 optimal weight: 30.0000 chunk 287 optimal weight: 9.9990 chunk 427 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 506 optimal weight: 40.0000 chunk 316 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 33 GLN B 708 ASN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 GLN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43535 Z= 0.232 Angle : 0.702 11.061 59330 Z= 0.354 Chirality : 0.046 0.171 6855 Planarity : 0.005 0.071 7560 Dihedral : 6.133 58.492 5950 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.28 % Favored : 89.12 % Rotamer: Outliers : 1.51 % Allowed : 17.22 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 5265 helix: -1.54 (0.12), residues: 1605 sheet: -0.40 (0.19), residues: 750 loop : -2.83 (0.10), residues: 2910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 460 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 509 average time/residue: 0.5196 time to fit residues: 449.6873 Evaluate side-chains 456 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 418 time to evaluate : 4.601 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3835 time to fit residues: 34.8208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 313 optimal weight: 30.0000 chunk 202 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 152 optimal weight: 0.0000 chunk 99 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 397 optimal weight: 7.9990 overall best weight: 3.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 HIS B 607 ASN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 ASN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43535 Z= 0.182 Angle : 0.680 12.731 59330 Z= 0.340 Chirality : 0.045 0.176 6855 Planarity : 0.005 0.062 7560 Dihedral : 5.882 57.244 5950 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.16 % Favored : 89.17 % Rotamer: Outliers : 0.93 % Allowed : 18.13 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.91 (0.11), residues: 5265 helix: -1.43 (0.12), residues: 1620 sheet: -0.19 (0.20), residues: 695 loop : -2.78 (0.10), residues: 2950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 457 time to evaluate : 4.824 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 488 average time/residue: 0.5057 time to fit residues: 422.1304 Evaluate side-chains 434 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 416 time to evaluate : 5.219 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4468 time to fit residues: 20.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 460 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 471 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 205 optimal weight: 30.0000 chunk 370 optimal weight: 0.0870 chunk 144 optimal weight: 20.0000 chunk 426 optimal weight: 0.7980 chunk 445 optimal weight: 2.9990 chunk 469 optimal weight: 0.5980 overall best weight: 2.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 492 HIS B 607 ASN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN D 905 GLN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43535 Z= 0.164 Angle : 0.678 11.061 59330 Z= 0.335 Chirality : 0.044 0.204 6855 Planarity : 0.005 0.065 7560 Dihedral : 5.631 59.278 5950 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.97 % Favored : 89.36 % Rotamer: Outliers : 0.40 % Allowed : 18.83 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 5265 helix: -1.22 (0.12), residues: 1615 sheet: -0.35 (0.19), residues: 775 loop : -2.65 (0.11), residues: 2875 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 457 time to evaluate : 5.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 471 average time/residue: 0.5112 time to fit residues: 413.3215 Evaluate side-chains 427 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 420 time to evaluate : 4.432 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5386 time to fit residues: 12.2557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 309 optimal weight: 8.9990 chunk 498 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 523 optimal weight: 10.0000 chunk 481 optimal weight: 7.9990 chunk 416 optimal weight: 6.9990 chunk 43 optimal weight: 40.0000 chunk 321 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN A 753 GLN A 905 GLN A 939 GLN B 492 HIS B 623 GLN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D 916 ASN E 607 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43535 Z= 0.272 Angle : 0.755 13.036 59330 Z= 0.377 Chirality : 0.047 0.197 6855 Planarity : 0.005 0.064 7560 Dihedral : 6.043 59.163 5950 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.07 % Favored : 88.24 % Rotamer: Outliers : 0.62 % Allowed : 18.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.11), residues: 5265 helix: -1.31 (0.12), residues: 1590 sheet: -0.25 (0.20), residues: 700 loop : -2.75 (0.10), residues: 2975 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 431 time to evaluate : 4.995 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 447 average time/residue: 0.5085 time to fit residues: 391.7812 Evaluate side-chains 420 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 402 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4624 time to fit residues: 21.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 330 optimal weight: 9.9990 chunk 443 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 417 optimal weight: 7.9990 chunk 174 optimal weight: 0.2980 chunk 428 optimal weight: 0.2980 chunk 52 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 HIS ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.146782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134697 restraints weight = 84297.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135167 restraints weight = 74778.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136506 restraints weight = 59780.159| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43535 Z= 0.191 Angle : 0.710 12.949 59330 Z= 0.350 Chirality : 0.045 0.180 6855 Planarity : 0.005 0.060 7560 Dihedral : 5.783 58.957 5950 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.95 % Favored : 89.40 % Rotamer: Outliers : 0.38 % Allowed : 19.30 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.11), residues: 5265 helix: -1.25 (0.12), residues: 1620 sheet: -0.10 (0.20), residues: 695 loop : -2.70 (0.11), residues: 2950 =============================================================================== Job complete usr+sys time: 9821.11 seconds wall clock time: 179 minutes 32.41 seconds (10772.41 seconds total)