Starting phenix.real_space_refine on Sun Mar 24 15:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/03_2024/3j6q_5926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/03_2024/3j6q_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_5926/03_2024/3j6q_5926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/03_2024/3j6q_5926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/03_2024/3j6q_5926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/03_2024/3j6q_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-dev-5265/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: 21.03, 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: 14.13 Conformation dependent library (CDL) restraints added in 7.4 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: 10.74 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: 15.78 Time building geometry restraints manager: 15.47 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: 5.980 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: 0.040 Extract box with map and model: 28.710 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 103.020 Find NCS groups from input model: 2.830 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.510 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 95 HIS 0.002 0.000 HIS C 806 PHE 0.003 0.001 PHE E 826 TYR 0.003 0.001 TYR C 38 ARG 0.009 0.003 ARG B 313 *********************** 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 : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ILE cc_start: 0.5189 (pt) cc_final: 0.4542 (pt) REVERT: A 481 ASP cc_start: 0.1677 (OUTLIER) cc_final: 0.1305 (t70) REVERT: A 1056 VAL cc_start: 0.7387 (p) cc_final: 0.7126 (p) REVERT: B 411 ILE cc_start: 0.5013 (pt) cc_final: 0.4493 (pt) REVERT: B 481 ASP cc_start: 0.1917 (OUTLIER) cc_final: 0.1571 (t70) REVERT: B 812 VAL cc_start: 0.7481 (t) cc_final: 0.7208 (m) REVERT: B 886 ARG cc_start: 0.4226 (mtt180) cc_final: 0.3872 (mtm-85) REVERT: C 411 ILE cc_start: 0.5425 (pt) cc_final: 0.5079 (pt) REVERT: C 481 ASP cc_start: 0.2183 (OUTLIER) cc_final: 0.1633 (t70) REVERT: C 812 VAL cc_start: 0.7774 (t) cc_final: 0.7490 (m) REVERT: C 1056 VAL cc_start: 0.7488 (p) cc_final: 0.7196 (p) REVERT: D 411 ILE cc_start: 0.5181 (pt) cc_final: 0.4106 (pt) REVERT: D 1056 VAL cc_start: 0.7278 (p) cc_final: 0.6933 (p) REVERT: E 411 ILE cc_start: 0.5347 (pt) cc_final: 0.5059 (pt) REVERT: E 481 ASP cc_start: 0.2766 (OUTLIER) cc_final: 0.2093 (t70) outliers start: 30 outliers final: 3 residues processed: 1463 average time/residue: 0.5737 time to fit residues: 1329.5271 Evaluate side-chains 671 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 664 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain E residue 481 ASP 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: 9.9990 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 A 857 GLN B 8 ASN B 33 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS B 544 ASN B 623 GLN 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 270 GLN D 281 ASN ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6305 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43535 Z= 0.225 Angle : 0.763 9.428 59330 Z= 0.390 Chirality : 0.047 0.259 6855 Planarity : 0.006 0.078 7560 Dihedral : 7.320 87.938 5967 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.20 % Rotamer: Outliers : 3.59 % Allowed : 11.15 % Favored : 85.27 % 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: -3.69 (0.10), residues: 5265 helix: -2.57 (0.11), residues: 1345 sheet: -0.58 (0.18), residues: 795 loop : -3.06 (0.10), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 772 HIS 0.012 0.002 HIS A 332 PHE 0.017 0.002 PHE A1046 TYR 0.024 0.002 TYR A1031 ARG 0.023 0.001 ARG B1057 *********************** 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 914 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 745 time to evaluate : 5.210 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: A 47 ARG cc_start: 0.6009 (ptt-90) cc_final: 0.5512 (ttt90) REVERT: A 405 MET cc_start: 0.6195 (ppp) cc_final: 0.5744 (ppp) REVERT: A 414 GLU cc_start: 0.7006 (mp0) cc_final: 0.6241 (tm-30) REVERT: A 768 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6794 (mm-30) REVERT: A 779 ASN cc_start: 0.6914 (m110) cc_final: 0.6674 (m-40) REVERT: A 812 VAL cc_start: 0.7702 (t) cc_final: 0.7277 (m) REVERT: A 1056 VAL cc_start: 0.7542 (p) cc_final: 0.7063 (p) REVERT: B 100 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7339 (p-80) REVERT: B 812 VAL cc_start: 0.7521 (t) cc_final: 0.7210 (m) REVERT: C 405 MET cc_start: 0.6496 (pmm) cc_final: 0.5804 (ppp) REVERT: C 455 MET cc_start: 0.6649 (tpp) cc_final: 0.6384 (tpp) REVERT: C 762 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7514 (mp) REVERT: C 812 VAL cc_start: 0.7850 (t) cc_final: 0.7506 (m) REVERT: C 1056 VAL cc_start: 0.7222 (p) cc_final: 0.6657 (p) REVERT: D 783 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 812 VAL cc_start: 0.7527 (t) cc_final: 0.7149 (m) REVERT: D 938 MET cc_start: 0.5669 (mmm) cc_final: 0.5109 (ptm) REVERT: D 1056 VAL cc_start: 0.7117 (p) cc_final: 0.6847 (p) REVERT: E 405 MET cc_start: 0.6004 (ppp) cc_final: 0.5236 (ppp) REVERT: E 812 VAL cc_start: 0.7630 (t) cc_final: 0.7342 (m) outliers start: 169 outliers final: 99 residues processed: 875 average time/residue: 0.5538 time to fit residues: 809.7355 Evaluate side-chains 652 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 550 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 783 ILE Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 800 SER Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 264 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 131 optimal weight: 0.0060 chunk 477 optimal weight: 9.9990 chunk 515 optimal weight: 40.0000 chunk 425 optimal weight: 9.9990 chunk 473 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 383 optimal weight: 30.0000 overall best weight: 6.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 49 HIS A 93 HIS A 492 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS A 857 GLN B 49 HIS B 212 HIS ** 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 61 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 212 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43535 Z= 0.260 Angle : 0.747 9.608 59330 Z= 0.386 Chirality : 0.047 0.260 6855 Planarity : 0.006 0.114 7560 Dihedral : 6.314 59.779 5950 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.12 % Favored : 87.07 % Rotamer: Outliers : 4.59 % Allowed : 12.27 % Favored : 83.14 % 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: -3.34 (0.10), residues: 5265 helix: -2.12 (0.12), residues: 1460 sheet: -0.34 (0.20), residues: 735 loop : -2.89 (0.10), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 213 HIS 0.009 0.002 HIS C 837 PHE 0.020 0.002 PHE C 575 TYR 0.019 0.002 TYR B 919 ARG 0.006 0.001 ARG C 47 *********************** 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 801 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 585 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 405 MET cc_start: 0.6142 (ppp) cc_final: 0.5115 (ppp) REVERT: A 458 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: A 481 ASP cc_start: 0.2805 (OUTLIER) cc_final: 0.2028 (t70) REVERT: A 768 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 779 ASN cc_start: 0.7095 (m110) cc_final: 0.6755 (m-40) REVERT: B 100 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7174 (p-80) REVERT: B 362 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.3759 (tmm) REVERT: B 481 ASP cc_start: 0.3387 (OUTLIER) cc_final: 0.1921 (t70) REVERT: B 812 VAL cc_start: 0.7475 (t) cc_final: 0.7051 (m) REVERT: B 829 MET cc_start: 0.7145 (mtp) cc_final: 0.6856 (mtp) REVERT: B 898 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: C 362 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.4214 (tmm) REVERT: C 481 ASP cc_start: 0.2677 (OUTLIER) cc_final: 0.2045 (t70) REVERT: C 683 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: D 523 MET cc_start: 0.6827 (tpp) cc_final: 0.6494 (tpt) REVERT: D 783 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 1006 MET cc_start: 0.6505 (ptm) cc_final: 0.6276 (ptm) REVERT: E 78 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: E 300 LEU cc_start: 0.8498 (tp) cc_final: 0.8205 (tt) REVERT: E 405 MET cc_start: 0.5906 (ppp) cc_final: 0.5468 (ppp) REVERT: E 481 ASP cc_start: 0.3477 (OUTLIER) cc_final: 0.2334 (t70) REVERT: E 829 MET cc_start: 0.6881 (mtp) cc_final: 0.6581 (mtp) outliers start: 216 outliers final: 138 residues processed: 744 average time/residue: 0.4867 time to fit residues: 612.8432 Evaluate side-chains 631 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 480 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 957 VAL Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 783 ILE Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 623 GLN Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 30.0000 chunk 359 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 479 optimal weight: 8.9990 chunk 507 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 454 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 212 HIS ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 61 ASN B 281 ASN B 492 HIS B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN B1048 HIS ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS D 21 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 21 GLN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 HIS E 434 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 43535 Z= 0.427 Angle : 0.898 12.794 59330 Z= 0.464 Chirality : 0.052 0.248 6855 Planarity : 0.007 0.090 7560 Dihedral : 7.266 69.901 5950 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.12 % Favored : 87.01 % Rotamer: Outliers : 5.99 % Allowed : 14.01 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.10), residues: 5265 helix: -2.32 (0.11), residues: 1585 sheet: -0.57 (0.19), residues: 755 loop : -3.12 (0.10), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 213 HIS 0.010 0.002 HIS E 837 PHE 0.027 0.003 PHE C 60 TYR 0.031 0.003 TYR A 656 ARG 0.010 0.001 ARG D 953 *********************** 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 799 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 517 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.8139 (t-100) REVERT: A 415 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5927 (t70) REVERT: A 455 MET cc_start: 0.6952 (tpp) cc_final: 0.5852 (tpp) REVERT: A 479 LYS cc_start: 0.4946 (OUTLIER) cc_final: 0.4345 (pttt) REVERT: A 481 ASP cc_start: 0.3174 (OUTLIER) cc_final: 0.2786 (t70) REVERT: A 768 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 829 MET cc_start: 0.7094 (mtp) cc_final: 0.6593 (mtp) REVERT: A 1006 MET cc_start: 0.6375 (ptm) cc_final: 0.6054 (ptp) REVERT: B 95 TRP cc_start: 0.8712 (OUTLIER) cc_final: 0.8112 (t-100) REVERT: B 100 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7217 (p-80) REVERT: B 475 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6402 (ttm-80) REVERT: B 481 ASP cc_start: 0.3553 (OUTLIER) cc_final: 0.3108 (t70) REVERT: B 716 MET cc_start: 0.5354 (mmm) cc_final: 0.5127 (mmm) REVERT: B 828 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7110 (m-10) REVERT: B 898 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: C 78 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: C 455 MET cc_start: 0.7041 (tpp) cc_final: 0.6730 (ttt) REVERT: C 481 ASP cc_start: 0.3539 (OUTLIER) cc_final: 0.2710 (t70) REVERT: C 828 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: C 992 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.3860 (m-10) REVERT: D 47 ARG cc_start: 0.7220 (ptt-90) cc_final: 0.6882 (mtm180) REVERT: D 78 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: D 475 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.5745 (ttm-80) REVERT: D 479 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4404 (pttt) REVERT: D 523 MET cc_start: 0.7171 (tpp) cc_final: 0.6867 (tpp) REVERT: D 828 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: D 898 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: D 1006 MET cc_start: 0.6304 (ptm) cc_final: 0.6051 (ptm) REVERT: E 78 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: E 95 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.8032 (t-100) REVERT: E 132 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7225 (tp40) REVERT: E 455 MET cc_start: 0.6699 (tpt) cc_final: 0.6145 (tpt) REVERT: E 475 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5929 (ttm-80) REVERT: E 481 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.3257 (t70) REVERT: E 485 MET cc_start: 0.6843 (tpp) cc_final: 0.6291 (mmp) REVERT: E 604 ILE cc_start: 0.4140 (OUTLIER) cc_final: 0.3479 (mm) REVERT: E 829 MET cc_start: 0.7330 (mtp) cc_final: 0.6540 (mtp) REVERT: E 998 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5424 (tp) outliers start: 282 outliers final: 173 residues processed: 734 average time/residue: 0.4962 time to fit residues: 614.4447 Evaluate side-chains 623 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 424 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 627 SER Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 898 GLU Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 719 VAL Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 977 HIS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1024 LEU Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 422 optimal weight: 0.1980 chunk 288 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 433 optimal weight: 0.8980 chunk 350 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 259 optimal weight: 4.9990 chunk 455 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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** A 708 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 ASN C 905 GLN C 945 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 61 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: 0.6857 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43535 Z= 0.180 Angle : 0.693 10.530 59330 Z= 0.351 Chirality : 0.046 0.258 6855 Planarity : 0.005 0.065 7560 Dihedral : 6.290 58.135 5950 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.16 % Favored : 89.17 % Rotamer: Outliers : 3.61 % Allowed : 17.30 % Favored : 79.09 % 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: -3.32 (0.11), residues: 5265 helix: -1.81 (0.12), residues: 1540 sheet: -0.58 (0.19), residues: 760 loop : -3.00 (0.10), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 213 HIS 0.004 0.001 HIS A 332 PHE 0.026 0.001 PHE C 505 TYR 0.020 0.001 TYR B 688 ARG 0.010 0.000 ARG C1057 *********************** 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 656 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 486 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6666 (tpp) cc_final: 0.5804 (tpp) REVERT: A 768 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 855 MET cc_start: 0.5987 (mmp) cc_final: 0.5784 (mmm) REVERT: A 1006 MET cc_start: 0.6316 (ptm) cc_final: 0.5962 (ptp) REVERT: B 54 LEU cc_start: 0.7359 (pp) cc_final: 0.6978 (tp) REVERT: B 100 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6973 (p-80) REVERT: B 102 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 362 MET cc_start: 0.5478 (tmt) cc_final: 0.4867 (tmt) REVERT: B 540 LYS cc_start: 0.6962 (mmtm) cc_final: 0.6620 (mmmt) REVERT: B 828 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6648 (m-10) REVERT: B 898 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: C 78 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.4855 (m-80) REVERT: C 167 THR cc_start: 0.7845 (m) cc_final: 0.7603 (m) REVERT: C 267 THR cc_start: 0.8471 (p) cc_final: 0.8180 (t) REVERT: C 362 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.4904 (tmt) REVERT: C 828 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6110 (m-10) REVERT: D 47 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.6807 (mtm180) REVERT: D 78 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.4940 (m-80) REVERT: D 409 MET cc_start: 0.6190 (tmm) cc_final: 0.5672 (tmm) REVERT: D 479 LYS cc_start: 0.5079 (OUTLIER) cc_final: 0.4105 (pttt) REVERT: D 587 MET cc_start: 0.6549 (mtp) cc_final: 0.6218 (mtp) REVERT: D 784 ILE cc_start: 0.7127 (mt) cc_final: 0.6926 (mt) REVERT: D 828 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.6002 (m-10) REVERT: E 78 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: E 455 MET cc_start: 0.6680 (tpt) cc_final: 0.6245 (tpt) REVERT: E 587 MET cc_start: 0.6961 (mtt) cc_final: 0.6536 (mtt) REVERT: E 604 ILE cc_start: 0.3919 (tp) cc_final: 0.3551 (tp) REVERT: E 829 MET cc_start: 0.6713 (mtp) cc_final: 0.6435 (mtp) REVERT: E 839 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8083 (mm) REVERT: E 950 MET cc_start: 0.4265 (mmm) cc_final: 0.4057 (mmm) outliers start: 170 outliers final: 117 residues processed: 615 average time/residue: 0.5148 time to fit residues: 541.4457 Evaluate side-chains 560 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 431 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 627 SER Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 6.9990 chunk 456 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 507 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 HIS B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 ASN ** B 779 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 ASN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 ASN E 753 GLN ** E 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43535 Z= 0.197 Angle : 0.682 9.922 59330 Z= 0.346 Chirality : 0.045 0.171 6855 Planarity : 0.005 0.071 7560 Dihedral : 6.091 58.169 5950 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.77 % Favored : 88.57 % Rotamer: Outliers : 3.93 % Allowed : 17.54 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.11), residues: 5265 helix: -1.56 (0.13), residues: 1520 sheet: -0.33 (0.19), residues: 745 loop : -2.93 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 213 HIS 0.014 0.001 HIS C 492 PHE 0.016 0.001 PHE D 505 TYR 0.018 0.001 TYR B 688 ARG 0.007 0.000 ARG B 599 *********************** 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 634 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 449 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7742 (mt) REVERT: A 95 TRP cc_start: 0.8702 (OUTLIER) cc_final: 0.7869 (t-100) REVERT: A 455 MET cc_start: 0.6642 (tpp) cc_final: 0.5909 (tpp) REVERT: A 479 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.3843 (pttt) REVERT: A 481 ASP cc_start: 0.3302 (OUTLIER) cc_final: 0.2618 (t70) REVERT: A 657 MET cc_start: 0.6636 (mtp) cc_final: 0.6040 (mtp) REVERT: A 768 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 917 SER cc_start: 0.4949 (m) cc_final: 0.4732 (p) REVERT: A 1006 MET cc_start: 0.6243 (ptm) cc_final: 0.5886 (ptp) REVERT: B 54 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7015 (tp) REVERT: B 100 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.6969 (p-80) REVERT: B 362 MET cc_start: 0.5444 (tmt) cc_final: 0.4780 (tmt) REVERT: B 483 MET cc_start: 0.5166 (ttp) cc_final: 0.4923 (ttm) REVERT: B 828 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6597 (m-10) REVERT: B 898 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: C 78 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: C 167 THR cc_start: 0.7916 (m) cc_final: 0.7636 (m) REVERT: C 267 THR cc_start: 0.8571 (p) cc_final: 0.8321 (t) REVERT: C 362 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.4773 (tmt) REVERT: C 455 MET cc_start: 0.7097 (tpp) cc_final: 0.6844 (ttm) REVERT: C 481 ASP cc_start: 0.3257 (OUTLIER) cc_final: 0.2626 (t70) REVERT: C 828 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6191 (m-10) REVERT: D 47 ARG cc_start: 0.7125 (ptt-90) cc_final: 0.6766 (mtm180) REVERT: D 78 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.4919 (m-80) REVERT: D 409 MET cc_start: 0.5935 (tmm) cc_final: 0.5442 (tmm) REVERT: D 479 LYS cc_start: 0.5078 (OUTLIER) cc_final: 0.3952 (pttt) REVERT: D 828 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: D 950 MET cc_start: 0.4101 (mmm) cc_final: 0.3899 (mmm) REVERT: E 78 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.5967 (m-80) REVERT: E 455 MET cc_start: 0.6745 (tpt) cc_final: 0.6345 (tpt) REVERT: E 481 ASP cc_start: 0.3843 (OUTLIER) cc_final: 0.2484 (t70) REVERT: E 587 MET cc_start: 0.7004 (mtt) cc_final: 0.6583 (mtp) REVERT: E 604 ILE cc_start: 0.3892 (tp) cc_final: 0.3250 (mm) REVERT: E 829 MET cc_start: 0.6841 (mtp) cc_final: 0.6535 (mtp) outliers start: 185 outliers final: 130 residues processed: 585 average time/residue: 0.4667 time to fit residues: 470.8832 Evaluate side-chains 573 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 426 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 489 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 289 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 427 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 506 optimal weight: 0.0870 chunk 316 optimal weight: 7.9990 chunk 308 optimal weight: 40.0000 chunk 233 optimal weight: 9.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS C 548 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.7399 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= 0.183 Angle : 0.672 10.848 59330 Z= 0.337 Chirality : 0.045 0.173 6855 Planarity : 0.005 0.063 7560 Dihedral : 5.940 59.901 5950 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.48 % Favored : 88.87 % Rotamer: Outliers : 4.03 % Allowed : 17.22 % Favored : 78.75 % 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: -3.00 (0.11), residues: 5265 helix: -1.46 (0.13), residues: 1555 sheet: -0.51 (0.19), residues: 775 loop : -2.82 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.007 0.001 HIS E 492 PHE 0.014 0.001 PHE B 505 TYR 0.017 0.001 TYR B 688 ARG 0.005 0.000 ARG B 599 *********************** 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 644 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 454 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 479 LYS cc_start: 0.4803 (OUTLIER) cc_final: 0.3874 (pmtt) REVERT: A 481 ASP cc_start: 0.3549 (OUTLIER) cc_final: 0.2820 (t70) REVERT: A 545 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6517 (t80) REVERT: A 657 MET cc_start: 0.6679 (mtp) cc_final: 0.6126 (mtp) REVERT: A 768 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 1006 MET cc_start: 0.6217 (ptm) cc_final: 0.5891 (ptp) REVERT: B 54 LEU cc_start: 0.7382 (pp) cc_final: 0.7041 (tp) REVERT: B 95 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7781 (t-100) REVERT: B 100 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7035 (p-80) REVERT: B 475 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6279 (ttm-80) REVERT: B 481 ASP cc_start: 0.3631 (OUTLIER) cc_final: 0.3196 (t70) REVERT: B 828 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: B 898 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: C 78 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.4585 (m-80) REVERT: C 167 THR cc_start: 0.7912 (m) cc_final: 0.7674 (m) REVERT: C 267 THR cc_start: 0.8555 (p) cc_final: 0.8311 (t) REVERT: C 362 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.4776 (tmt) REVERT: C 455 MET cc_start: 0.7080 (tpp) cc_final: 0.6784 (ttp) REVERT: C 481 ASP cc_start: 0.3269 (OUTLIER) cc_final: 0.2792 (t70) REVERT: C 828 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6139 (m-10) REVERT: D 47 ARG cc_start: 0.6950 (ptt-90) cc_final: 0.6573 (mtm180) REVERT: D 78 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: D 409 MET cc_start: 0.5743 (tmm) cc_final: 0.5409 (tmm) REVERT: D 475 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5727 (ttm-80) REVERT: D 479 LYS cc_start: 0.5042 (OUTLIER) cc_final: 0.3908 (pttt) REVERT: D 828 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6322 (m-10) REVERT: D 855 MET cc_start: 0.5140 (mmm) cc_final: 0.4904 (mmt) REVERT: E 78 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: E 455 MET cc_start: 0.6772 (tpt) cc_final: 0.6465 (tpt) REVERT: E 481 ASP cc_start: 0.3825 (OUTLIER) cc_final: 0.3049 (t70) REVERT: E 587 MET cc_start: 0.6917 (mtt) cc_final: 0.6474 (mtp) REVERT: E 604 ILE cc_start: 0.3664 (tp) cc_final: 0.3337 (tp) REVERT: E 753 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7569 (mm-40) REVERT: E 829 MET cc_start: 0.6969 (mtp) cc_final: 0.6710 (mtp) REVERT: E 839 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mm) outliers start: 190 outliers final: 133 residues processed: 593 average time/residue: 0.4960 time to fit residues: 506.9909 Evaluate side-chains 585 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 431 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL 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: 1.9990 chunk 152 optimal weight: 7.9990 chunk 99 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43535 Z= 0.201 Angle : 0.689 12.994 59330 Z= 0.345 Chirality : 0.045 0.212 6855 Planarity : 0.005 0.068 7560 Dihedral : 5.909 59.202 5950 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.67 % Favored : 88.68 % Rotamer: Outliers : 4.03 % Allowed : 17.56 % Favored : 78.41 % 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: -2.91 (0.11), residues: 5265 helix: -1.37 (0.13), residues: 1550 sheet: -0.56 (0.19), residues: 780 loop : -2.75 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.006 0.001 HIS E 492 PHE 0.019 0.001 PHE B 42 TYR 0.016 0.001 TYR B 688 ARG 0.004 0.000 ARG B 599 *********************** 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 637 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 447 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7582 (mt) REVERT: A 95 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7896 (t-100) REVERT: A 479 LYS cc_start: 0.4916 (OUTLIER) cc_final: 0.4118 (pmtt) REVERT: A 481 ASP cc_start: 0.3389 (OUTLIER) cc_final: 0.2740 (t70) REVERT: A 545 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6539 (t80) REVERT: A 657 MET cc_start: 0.6607 (mtp) cc_final: 0.6057 (mtp) REVERT: A 768 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 1006 MET cc_start: 0.6275 (ptm) cc_final: 0.5941 (ptp) REVERT: A 1025 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7958 (mt) REVERT: B 54 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7099 (tp) REVERT: B 95 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7849 (t-100) REVERT: B 100 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7008 (p-80) REVERT: B 475 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6381 (ttm-80) REVERT: B 481 ASP cc_start: 0.3645 (OUTLIER) cc_final: 0.3264 (t70) REVERT: B 657 MET cc_start: 0.6894 (mtt) cc_final: 0.6370 (mtp) REVERT: B 828 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6655 (m-10) REVERT: B 898 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: C 78 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.4582 (m-80) REVERT: C 167 THR cc_start: 0.7949 (m) cc_final: 0.7741 (m) REVERT: C 267 THR cc_start: 0.8582 (p) cc_final: 0.8327 (t) REVERT: C 362 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.4677 (tmt) REVERT: C 455 MET cc_start: 0.7135 (tpp) cc_final: 0.6699 (ttt) REVERT: C 481 ASP cc_start: 0.3612 (OUTLIER) cc_final: 0.3202 (t70) REVERT: C 828 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: D 47 ARG cc_start: 0.6997 (ptt-90) cc_final: 0.6592 (mtm180) REVERT: D 78 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: D 409 MET cc_start: 0.5901 (tmm) cc_final: 0.5474 (tmm) REVERT: D 475 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.5817 (ttm-80) REVERT: D 479 LYS cc_start: 0.5050 (OUTLIER) cc_final: 0.3897 (pttt) REVERT: D 828 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6159 (m-10) REVERT: D 855 MET cc_start: 0.4946 (mmm) cc_final: 0.4691 (mmt) REVERT: E 78 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5856 (m-80) REVERT: E 132 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7023 (tp40) REVERT: E 455 MET cc_start: 0.6898 (tpt) cc_final: 0.6607 (tpt) REVERT: E 481 ASP cc_start: 0.3771 (OUTLIER) cc_final: 0.3047 (t70) REVERT: E 604 ILE cc_start: 0.3657 (tp) cc_final: 0.3363 (tp) REVERT: E 950 MET cc_start: 0.3989 (mmm) cc_final: 0.3625 (mmm) outliers start: 190 outliers final: 142 residues processed: 589 average time/residue: 0.4749 time to fit residues: 483.1467 Evaluate side-chains 595 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 429 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 460 optimal weight: 5.9990 chunk 484 optimal weight: 9.9990 chunk 442 optimal weight: 10.0000 chunk 471 optimal weight: 40.0000 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 426 optimal weight: 1.9990 chunk 445 optimal weight: 0.0170 chunk 469 optimal weight: 7.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- 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 ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 905 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: 0.6903 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43535 Z= 0.187 Angle : 0.686 12.517 59330 Z= 0.340 Chirality : 0.045 0.173 6855 Planarity : 0.005 0.066 7560 Dihedral : 5.795 58.390 5950 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.33 % Favored : 89.02 % Rotamer: Outliers : 3.82 % Allowed : 17.98 % Favored : 78.20 % 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: -2.86 (0.11), residues: 5265 helix: -1.41 (0.12), residues: 1580 sheet: -0.23 (0.20), residues: 700 loop : -2.71 (0.11), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.005 0.001 HIS E 492 PHE 0.022 0.001 PHE E 505 TYR 0.018 0.001 TYR B 59 ARG 0.004 0.000 ARG B 599 *********************** 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 622 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 442 time to evaluate : 5.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7792 (t-100) REVERT: A 479 LYS cc_start: 0.4734 (OUTLIER) cc_final: 0.3905 (pttt) REVERT: A 481 ASP cc_start: 0.3510 (OUTLIER) cc_final: 0.2744 (t70) REVERT: A 545 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 657 MET cc_start: 0.6590 (mtp) cc_final: 0.6035 (mtp) REVERT: A 683 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: A 768 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6863 (mm-30) REVERT: A 1006 MET cc_start: 0.6270 (ptm) cc_final: 0.5924 (ptp) REVERT: A 1025 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7964 (mt) REVERT: B 95 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.7848 (t-100) REVERT: B 100 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.6956 (p-80) REVERT: B 475 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6367 (ttm-80) REVERT: B 481 ASP cc_start: 0.3703 (OUTLIER) cc_final: 0.3369 (t70) REVERT: B 828 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: B 898 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: C 54 LEU cc_start: 0.6929 (pt) cc_final: 0.6231 (tp) REVERT: C 78 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.4632 (m-80) REVERT: C 257 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6986 (tp) REVERT: C 267 THR cc_start: 0.8558 (p) cc_final: 0.8301 (t) REVERT: C 362 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.4647 (tmt) REVERT: C 455 MET cc_start: 0.7067 (tpp) cc_final: 0.6819 (ttm) REVERT: C 481 ASP cc_start: 0.3582 (OUTLIER) cc_final: 0.3193 (t70) REVERT: C 492 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.5457 (p-80) REVERT: C 828 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: C 992 TYR cc_start: 0.4562 (OUTLIER) cc_final: 0.3935 (m-10) REVERT: D 47 ARG cc_start: 0.6971 (ptt-90) cc_final: 0.6549 (mtm180) REVERT: D 78 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.4765 (m-80) REVERT: D 409 MET cc_start: 0.5842 (tmm) cc_final: 0.5470 (tmm) REVERT: D 475 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5816 (ttm-80) REVERT: D 479 LYS cc_start: 0.4953 (OUTLIER) cc_final: 0.3854 (pttt) REVERT: D 828 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: D 855 MET cc_start: 0.4938 (mmm) cc_final: 0.4449 (mmt) REVERT: E 78 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: E 455 MET cc_start: 0.6949 (tpt) cc_final: 0.6680 (tpt) REVERT: E 481 ASP cc_start: 0.4061 (OUTLIER) cc_final: 0.3274 (t70) REVERT: E 604 ILE cc_start: 0.3641 (tp) cc_final: 0.3356 (tp) REVERT: E 950 MET cc_start: 0.3952 (mmm) cc_final: 0.3600 (mmm) outliers start: 180 outliers final: 144 residues processed: 574 average time/residue: 0.4812 time to fit residues: 477.1884 Evaluate side-chains 594 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 425 time to evaluate : 4.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 724 MET Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 912 ASP Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1042 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 309 optimal weight: 10.0000 chunk 498 optimal weight: 1.9990 chunk 304 optimal weight: 40.0000 chunk 236 optimal weight: 3.9990 chunk 346 optimal weight: 10.0000 chunk 523 optimal weight: 0.1980 chunk 481 optimal weight: 5.9990 chunk 416 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 321 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 overall best weight: 4.4390 ------------------------------------------------------------------------------- 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** A 939 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** 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: 0.6910 moved from start: 0.7832 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= 0.188 Angle : 0.688 12.355 59330 Z= 0.340 Chirality : 0.045 0.174 6855 Planarity : 0.005 0.066 7560 Dihedral : 5.732 58.065 5950 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.45 % Favored : 88.91 % Rotamer: Outliers : 3.76 % Allowed : 18.26 % Favored : 77.98 % 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: -2.79 (0.11), residues: 5265 helix: -1.30 (0.13), residues: 1580 sheet: -0.21 (0.20), residues: 705 loop : -2.70 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS E 492 PHE 0.022 0.001 PHE E 505 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.000 ARG C 47 ********************** 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 620 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 443 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 95 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.7795 (t-100) REVERT: A 479 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.3835 (pttt) REVERT: A 481 ASP cc_start: 0.3478 (OUTLIER) cc_final: 0.2667 (t70) REVERT: A 545 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6516 (t80) REVERT: A 657 MET cc_start: 0.6551 (mtp) cc_final: 0.5995 (mtp) REVERT: A 768 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 1006 MET cc_start: 0.6276 (ptm) cc_final: 0.5930 (ptp) REVERT: A 1025 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7886 (mt) REVERT: B 95 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.7863 (t-100) REVERT: B 100 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.6943 (p-80) REVERT: B 475 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6401 (ttm-80) REVERT: B 481 ASP cc_start: 0.4131 (OUTLIER) cc_final: 0.3692 (t70) REVERT: B 784 ILE cc_start: 0.6810 (mt) cc_final: 0.6189 (mt) REVERT: B 828 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6680 (m-10) REVERT: B 898 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: C 54 LEU cc_start: 0.6905 (pt) cc_final: 0.6244 (tp) REVERT: C 78 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.4704 (m-80) REVERT: C 257 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7035 (tp) REVERT: C 267 THR cc_start: 0.8618 (p) cc_final: 0.8352 (t) REVERT: C 362 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.4662 (tmt) REVERT: C 455 MET cc_start: 0.7017 (tpp) cc_final: 0.6712 (ttt) REVERT: C 481 ASP cc_start: 0.3643 (OUTLIER) cc_final: 0.3226 (t70) REVERT: C 492 HIS cc_start: 0.5697 (OUTLIER) cc_final: 0.5453 (p-80) REVERT: C 828 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6253 (m-10) REVERT: D 47 ARG cc_start: 0.6950 (ptt-90) cc_final: 0.6524 (mtm180) REVERT: D 78 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.4739 (m-80) REVERT: D 409 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5490 (tmm) REVERT: D 475 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.5712 (ttm-80) REVERT: D 479 LYS cc_start: 0.4882 (OUTLIER) cc_final: 0.3734 (pttt) REVERT: D 828 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: D 855 MET cc_start: 0.5050 (mmm) cc_final: 0.4636 (mmt) REVERT: E 78 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: E 132 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7055 (tp40) REVERT: E 455 MET cc_start: 0.6996 (tpt) cc_final: 0.6769 (tpt) REVERT: E 481 ASP cc_start: 0.3994 (OUTLIER) cc_final: 0.3198 (t70) REVERT: E 604 ILE cc_start: 0.3535 (tp) cc_final: 0.3274 (tp) REVERT: E 950 MET cc_start: 0.4026 (mmm) cc_final: 0.3687 (mmm) outliers start: 177 outliers final: 143 residues processed: 575 average time/residue: 0.4769 time to fit residues: 472.1771 Evaluate side-chains 591 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 422 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 330 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 384 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 428 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 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 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.144064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131853 restraints weight = 84828.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132258 restraints weight = 77976.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.133490 restraints weight = 60056.251| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43535 Z= 0.248 Angle : 0.733 12.928 59330 Z= 0.365 Chirality : 0.047 0.207 6855 Planarity : 0.005 0.068 7560 Dihedral : 5.975 58.701 5950 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.30 % Favored : 88.07 % Rotamer: Outliers : 3.78 % Allowed : 18.45 % Favored : 77.77 % 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: -2.84 (0.11), residues: 5265 helix: -1.38 (0.13), residues: 1585 sheet: -0.20 (0.19), residues: 745 loop : -2.75 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.006 0.001 HIS E 49 PHE 0.025 0.002 PHE E 505 TYR 0.021 0.002 TYR B 59 ARG 0.007 0.000 ARG C 47 =============================================================================== Job complete usr+sys time: 10201.41 seconds wall clock time: 184 minutes 46.30 seconds (11086.30 seconds total)