Starting phenix.real_space_refine on Sat Dec 16 14:34:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bpb_30150/12_2023/7bpb_30150_updated.pdb" } resolution = 4.3 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= 0.000 sd= 0.070 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 30 5.49 5 S 180 5.16 5 C 22008 2.51 5 N 6252 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35238 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'ADP': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.37, per 1000 atoms: 0.52 Number of scatterers: 35238 At special positions: 0 Unit cell: (169.534, 185.629, 101.935, 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 180 16.00 P 30 15.00 O 6768 8.00 N 6252 7.00 C 22008 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.58 Conformation dependent library (CDL) restraints added in 6.9 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 30 sheets defined 39.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 526 through 534 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.985A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 585 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.447A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 759 " --> pdb=" O TYR A 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 444' Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 526 through 534 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 585 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 429 through 432 No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 440 through 444' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 526 through 534 Processing helix chain 'C' and resid 544 through 551 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 585 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 759 " --> pdb=" O TYR C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 335 removed outlier: 4.146A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 429 through 432 No H-bonds generated for 'chain 'D' and resid 429 through 432' Processing helix chain 'D' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 440 through 444' Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 544 through 551 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.983A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA D 585 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 686 through 713 removed outlier: 4.999A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.449A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 759 " --> pdb=" O TYR D 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 131 through 138 removed outlier: 4.682A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 335 removed outlier: 4.147A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 429 through 432 No H-bonds generated for 'chain 'E' and resid 429 through 432' Processing helix chain 'E' and resid 440 through 444 removed outlier: 3.582A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 440 through 444' Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 526 through 534 Processing helix chain 'E' and resid 544 through 551 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 579 through 585 removed outlier: 3.983A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 585 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 673 through 678 Processing helix chain 'E' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA E 759 " --> pdb=" O TYR E 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 131 through 138 removed outlier: 4.681A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.617A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 335 removed outlier: 4.146A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 429 through 432 No H-bonds generated for 'chain 'F' and resid 429 through 432' Processing helix chain 'F' and resid 440 through 444 removed outlier: 3.581A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 440 through 444' Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.834A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 526 through 534 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.984A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 585 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 673 through 678 Processing helix chain 'F' and resid 686 through 713 removed outlier: 4.998A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 761 removed outlier: 4.448A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 759 " --> pdb=" O TYR F 755 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 144 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 645 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A 517 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= G, first strand: chain 'B' and resid 144 through 147 Processing sheet with id= H, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 645 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 517 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 144 through 147 Processing sheet with id= M, first strand: chain 'C' and resid 151 through 156 removed outlier: 7.072A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 645 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 517 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= Q, first strand: chain 'D' and resid 144 through 147 Processing sheet with id= R, first strand: chain 'D' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE D 645 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR D 517 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= V, first strand: chain 'E' and resid 144 through 147 Processing sheet with id= W, first strand: chain 'E' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 9.439A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= AA, first strand: chain 'F' and resid 144 through 147 Processing sheet with id= AB, first strand: chain 'F' and resid 151 through 156 removed outlier: 7.073A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 9.440A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 642 through 645 removed outlier: 9.125A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 645 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR F 517 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1104 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.81 Time building geometry restraints manager: 14.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6660 1.32 - 1.45: 8002 1.45 - 1.57: 20828 1.57 - 1.70: 36 1.70 - 1.82: 294 Bond restraints: 35820 Sorted by residual: bond pdb=" O3A ANP E 901 " pdb=" PB ANP E 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP E 903 " pdb=" PB ANP E 903 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.57: 963 105.57 - 113.31: 19353 113.31 - 121.05: 18128 121.05 - 128.79: 9814 128.79 - 136.53: 168 Bond angle restraints: 48426 Sorted by residual: angle pdb=" PB ANP D 901 " pdb=" N3B ANP D 901 " pdb=" PG ANP D 901 " ideal model delta sigma weight residual 126.95 112.76 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" PB ANP E 901 " pdb=" N3B ANP E 901 " pdb=" PG ANP E 901 " ideal model delta sigma weight residual 126.95 112.78 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 112.79 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP E 903 " pdb=" N3B ANP E 903 " pdb=" PG ANP E 903 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP A 902 " pdb=" N3B ANP A 902 " pdb=" PG ANP A 902 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 ... (remaining 48421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 21778 34.85 - 69.71: 542 69.71 - 104.56: 36 104.56 - 139.41: 0 139.41 - 174.27: 6 Dihedral angle restraints: 22362 sinusoidal: 9564 harmonic: 12798 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.62 -91.62 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP C 902 " pdb=" O5' ADP C 902 " pdb=" PA ADP C 902 " pdb=" O2A ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.60 -91.60 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.59 -91.59 1 2.00e+01 2.50e-03 2.47e+01 ... (remaining 22359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3795 0.057 - 0.114: 1143 0.114 - 0.170: 355 0.170 - 0.227: 84 0.227 - 0.284: 41 Chirality restraints: 5418 Sorted by residual: chirality pdb=" C3' ANP A 902 " pdb=" C2' ANP A 902 " pdb=" C4' ANP A 902 " pdb=" O3' ANP A 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP E 903 " pdb=" C2' ANP E 903 " pdb=" C4' ANP E 903 " pdb=" O3' ANP E 903 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 5415 not shown) Planarity restraints: 6378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 545 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 544 " -0.062 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO D 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " -0.050 5.00e-02 4.00e+02 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 318 2.54 - 3.13: 24885 3.13 - 3.72: 55447 3.72 - 4.31: 69394 4.31 - 4.90: 110477 Nonbonded interactions: 260521 Sorted by model distance: nonbonded pdb=" CG ARG E 744 " pdb=" OE1 GLN F 763 " model vdw 1.956 3.440 nonbonded pdb=" OE1 GLN A 763 " pdb=" O ARG F 745 " model vdw 2.033 3.040 nonbonded pdb=" O ARG D 745 " pdb=" OE1 GLN E 763 " model vdw 2.038 3.040 nonbonded pdb=" CG ARG C 744 " pdb=" OE1 GLN D 763 " model vdw 2.071 3.440 nonbonded pdb=" O ARG C 745 " pdb=" OE1 GLN D 763 " model vdw 2.126 3.040 ... (remaining 260516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 766) selection = (chain 'B' and resid 20 through 766) selection = (chain 'C' and resid 20 through 766) selection = (chain 'D' and resid 20 through 766) selection = (chain 'E' and resid 20 through 766) selection = (chain 'F' and resid 20 through 766) } 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: 2.240 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: 0.060 Extract box with map and model: 12.220 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 92.060 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.220 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.151 35820 Z= 0.464 Angle : 1.118 14.194 48426 Z= 0.584 Chirality : 0.065 0.284 5418 Planarity : 0.009 0.093 6378 Dihedral : 16.099 174.269 14058 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.10), residues: 4416 helix: -3.32 (0.07), residues: 1890 sheet: -2.08 (0.17), residues: 774 loop : -2.21 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 454 HIS 0.015 0.002 HIS A 406 PHE 0.016 0.002 PHE A 152 TYR 0.014 0.002 TYR E 244 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 811 time to evaluate : 4.229 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 812 average time/residue: 0.5598 time to fit residues: 678.8320 Evaluate side-chains 516 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 3.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: