Starting phenix.real_space_refine on Fri Dec 15 09:10:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/12_2023/8ssa_40749_updated.pdb" } resolution = 3.88 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 12 5.49 5 S 168 5.16 5 C 20007 2.51 5 N 4985 2.21 5 O 5716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "B GLU 1103": "OE1" <-> "OE2" Residue "D GLU 1103": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30888 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "B" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "D" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU A1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'PCW': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU C1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'PCW': 2, 'SPD': 1} Inner-chain residues flagged as termini: ['pdbres="GLU D1103 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 16.03, per 1000 atoms: 0.52 Number of scatterers: 30888 At special positions: 0 Unit cell: (118.69, 145.25, 194.22, 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 168 16.00 P 12 15.00 O 5716 8.00 N 4985 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.02 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.57 Conformation dependent library (CDL) restraints added in 5.8 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 28 sheets defined 45.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.588A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.550A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.693A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.554A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.532A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.518A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.651A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.856A pdb=" N VAL A 327 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.646A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.698A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.241A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.751A pdb=" N PHE A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 4.039A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.559A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.808A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.826A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.988A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 765 Processing helix chain 'A' and resid 776 through 779 removed outlier: 3.535A pdb=" N GLY A 779 " --> pdb=" O LYS A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 794 through 819 removed outlier: 3.857A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.641A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 950 removed outlier: 3.516A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.791A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 3.886A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1031 removed outlier: 3.851A pdb=" N ILE A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.718A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.659A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.708A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.836A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.525A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.317A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.645A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.572A pdb=" N LEU B 284 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.946A pdb=" N GLU B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.875A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.538A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Proline residue: B 520 - end of helix No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 525 through 545 removed outlier: 4.163A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 4.042A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 removed outlier: 4.205A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.653A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.636A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.605A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 754 removed outlier: 3.851A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 4.371A pdb=" N LEU B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.646A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.589A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.549A pdb=" N ILE C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.692A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.554A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.531A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.519A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.652A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.856A pdb=" N VAL C 327 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 335 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.646A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.697A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 543 removed outlier: 4.240A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 584 removed outlier: 3.751A pdb=" N PHE C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 4.040A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 618 " --> pdb=" O SER C 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 removed outlier: 3.560A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 666 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.808A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.827A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 removed outlier: 3.987A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 Processing helix chain 'C' and resid 776 through 779 removed outlier: 3.536A pdb=" N GLY C 779 " --> pdb=" O LYS C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 779' Processing helix chain 'C' and resid 794 through 819 removed outlier: 3.857A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.640A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 851 " --> pdb=" O CYS C 847 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 950 removed outlier: 3.516A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.791A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 3.886A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1031 removed outlier: 3.850A pdb=" N ILE C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C1013 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.717A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.659A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.709A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.837A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.525A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 4.318A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.644A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.572A pdb=" N LEU D 284 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.947A pdb=" N GLU D 330 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.875A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 467 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.539A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) Proline residue: D 520 - end of helix No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 525 through 545 removed outlier: 4.162A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 4.041A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 623 removed outlier: 4.204A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.653A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.636A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 712 removed outlier: 3.606A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 754 removed outlier: 3.851A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 4.371A pdb=" N LEU D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 751 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 793 through 818 removed outlier: 3.646A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 23 removed outlier: 3.587A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 14 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.668A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 Processing helix chain 'E' and resid 69 through 84 removed outlier: 4.386A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 106 removed outlier: 3.546A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 127 through 157 removed outlier: 3.688A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 23 removed outlier: 3.584A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 removed outlier: 3.641A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 66 through 84 removed outlier: 4.214A pdb=" N VAL F 69 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.675A pdb=" N SER F 73 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS F 79 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.646A pdb=" N GLY F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 127 through 157 removed outlier: 3.691A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 140 " --> pdb=" O TRP F 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 132 through 137 removed outlier: 5.839A pdb=" N GLN A 159 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 135 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR A 161 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR A 137 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 163 " --> pdb=" O TYR A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 191 through 193 removed outlier: 6.446A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.685A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 395 through 399 removed outlier: 3.772A pdb=" N LYS A 441 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.680A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 45 through 50 removed outlier: 7.062A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 132 through 137 removed outlier: 5.779A pdb=" N GLN B 159 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 135 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR B 161 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 163 " --> pdb=" O TYR B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 243 through 246 removed outlier: 4.277A pdb=" N GLY B 244 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 345 " --> pdb=" O VAL B 338 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 397 through 399 Processing sheet with id= N, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 42 through 50 Processing sheet with id= P, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= Q, first strand: chain 'C' and resid 132 through 137 removed outlier: 5.839A pdb=" N GLN C 159 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR C 135 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR C 161 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR C 137 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 163 " --> pdb=" O TYR C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 191 through 193 removed outlier: 6.445A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.686A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 395 through 399 removed outlier: 3.771A pdb=" N LYS C 441 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 720 through 722 removed outlier: 3.679A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 45 through 50 removed outlier: 7.062A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 132 through 137 removed outlier: 5.778A pdb=" N GLN D 159 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR D 135 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR D 161 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR D 137 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 163 " --> pdb=" O TYR D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 243 through 246 removed outlier: 4.278A pdb=" N GLY D 244 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 397 through 399 Processing sheet with id= AB, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2928 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: 9.84 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5004 1.31 - 1.44: 8592 1.44 - 1.57: 17645 1.57 - 1.69: 26 1.69 - 1.82: 268 Bond restraints: 31535 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.423 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.416 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.422 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C11 PCW C1103 " pdb=" O3 PCW C1103 " ideal model delta sigma weight residual 1.326 1.415 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C31 PCW D1102 " pdb=" O2 PCW D1102 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 31530 not shown) Histogram of bond angle deviations from ideal: 95.65 - 103.74: 312 103.74 - 111.83: 13987 111.83 - 119.92: 14410 119.92 - 128.01: 13545 128.01 - 136.10: 280 Bond angle restraints: 42534 Sorted by residual: angle pdb=" C THR B 383 " pdb=" N GLU B 384 " pdb=" CA GLU B 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" C THR D 383 " pdb=" N GLU D 384 " pdb=" CA GLU D 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" N THR B 383 " pdb=" CA THR B 383 " pdb=" C THR B 383 " ideal model delta sigma weight residual 110.53 102.54 7.99 1.29e+00 6.01e-01 3.84e+01 angle pdb=" N THR D 383 " pdb=" CA THR D 383 " pdb=" C THR D 383 " ideal model delta sigma weight residual 110.53 102.55 7.98 1.29e+00 6.01e-01 3.83e+01 angle pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 ... (remaining 42529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 18350 35.38 - 70.77: 362 70.77 - 106.15: 37 106.15 - 141.53: 6 141.53 - 176.92: 10 Dihedral angle restraints: 18765 sinusoidal: 7683 harmonic: 11082 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual -180.00 -120.26 -59.74 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER D 403 " pdb=" C SER D 403 " pdb=" N PRO D 404 " pdb=" CA PRO D 404 " ideal model delta harmonic sigma weight residual -180.00 -125.12 -54.88 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 18762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3617 0.070 - 0.140: 931 0.140 - 0.210: 107 0.210 - 0.280: 21 0.280 - 0.350: 6 Chirality restraints: 4682 Sorted by residual: chirality pdb=" CB VAL B 395 " pdb=" CA VAL B 395 " pdb=" CG1 VAL B 395 " pdb=" CG2 VAL B 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB VAL D 395 " pdb=" CA VAL D 395 " pdb=" CG1 VAL D 395 " pdb=" CG2 VAL D 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 4679 not shown) Planarity restraints: 5306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO D 717 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO B 717 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 404 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.048 5.00e-02 4.00e+02 ... (remaining 5303 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4683 2.75 - 3.29: 30279 3.29 - 3.83: 52617 3.83 - 4.36: 62505 4.36 - 4.90: 101645 Nonbonded interactions: 251729 Sorted by model distance: nonbonded pdb=" OH TYR D 128 " pdb=" OG SER D 243 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.213 2.440 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.239 2.440 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU A 25 " pdb=" OG1 THR A 281 " model vdw 2.267 2.440 ... (remaining 251724 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 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 10 through 821 or resid 1101 through 1103)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 21.250 Check model and map are aligned: 0.260 Set scattering table: 0.300 Process input model: 79.050 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.210 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.105 31535 Z= 0.643 Angle : 1.318 14.561 42534 Z= 0.672 Chirality : 0.062 0.350 4682 Planarity : 0.008 0.135 5306 Dihedral : 14.930 176.918 11647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.37 % Favored : 87.63 % Rotamer: Outliers : 1.00 % Allowed : 6.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.92 % 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: -5.19 (0.10), residues: 3800 helix: -3.51 (0.07), residues: 1814 sheet: -3.49 (0.23), residues: 342 loop : -3.19 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 130 HIS 0.015 0.004 HIS A 214 PHE 0.037 0.004 PHE C 133 TYR 0.034 0.003 TYR E 149 ARG 0.008 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 747 time to evaluate : 3.495 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 6 residues processed: 772 average time/residue: 0.4106 time to fit residues: 493.6509 Evaluate side-chains 379 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 373 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2072 time to fit residues: 5.9056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: