Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 02:21:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdi_23773/05_2023/7mdi_23773_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 32 5.49 5 Mg 8 5.21 5 S 72 5.16 5 C 19572 2.51 5 N 5388 2.21 5 O 5528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ARG 737": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ARG 737": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 30608 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 35, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 429 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "B" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 35, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 429 Chain: "G" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "D" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 35, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 429 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "C" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 35, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 429 Chain: "H" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 16.28, per 1000 atoms: 0.53 Number of scatterers: 30608 At special positions: 0 Unit cell: (105.587, 223.972, 196.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 72 16.00 P 32 15.00 Mg 8 11.99 O 5528 8.00 N 5388 7.00 C 19572 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.27 Conformation dependent library (CDL) restraints added in 5.2 seconds 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 12 sheets defined 42.4% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.986A pdb=" N ASP A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.663A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.041A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.721A pdb=" N PHE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 4.167A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.809A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 removed outlier: 4.265A pdb=" N VAL A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 375 through 386 removed outlier: 3.585A pdb=" N GLU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.905A pdb=" N GLU A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 488 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A 496 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.624A pdb=" N THR A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.293A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 677 through 689 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 68 through 86 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 103 through 129 removed outlier: 3.809A pdb=" N TRP E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 137 No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 145 through 171 removed outlier: 4.774A pdb=" N ARG E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 205 removed outlier: 4.096A pdb=" N LYS E 192 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS E 193 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU E 196 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 4.043A pdb=" N SER E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 213 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 253 removed outlier: 4.391A pdb=" N ASP E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 268 Processing helix chain 'E' and resid 271 through 289 removed outlier: 4.054A pdb=" N ALA E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 108 through 114 removed outlier: 4.986A pdb=" N ASP B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.662A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.042A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.722A pdb=" N PHE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 removed outlier: 4.167A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.808A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 322 removed outlier: 4.265A pdb=" N VAL B 320 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.585A pdb=" N GLU B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 477 through 497 removed outlier: 3.905A pdb=" N GLU B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 488 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 497 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 3.624A pdb=" N THR B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.292A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 671 through 673 No H-bonds generated for 'chain 'B' and resid 671 through 673' Processing helix chain 'B' and resid 677 through 689 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 68 through 86 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 103 through 129 removed outlier: 3.808A pdb=" N TRP G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN G 129 " --> pdb=" O HIS G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 137 No H-bonds generated for 'chain 'G' and resid 134 through 137' Processing helix chain 'G' and resid 145 through 171 removed outlier: 4.774A pdb=" N ARG G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 161 " --> pdb=" O TYR G 157 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 205 removed outlier: 4.096A pdb=" N LYS G 192 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS G 193 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU G 196 " --> pdb=" O LYS G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 215 removed outlier: 4.043A pdb=" N SER G 212 " --> pdb=" O ARG G 208 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA G 214 " --> pdb=" O TYR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 253 removed outlier: 4.391A pdb=" N ASP G 234 " --> pdb=" O LYS G 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 235 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 268 Processing helix chain 'G' and resid 271 through 289 removed outlier: 4.053A pdb=" N ALA G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 317 Processing helix chain 'G' and resid 336 through 339 Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 57 through 68 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 108 through 114 removed outlier: 4.987A pdb=" N ASP D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.662A pdb=" N ASP D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.042A pdb=" N GLN D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.721A pdb=" N PHE D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 4.167A pdb=" N LYS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 198 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 214 No H-bonds generated for 'chain 'D' and resid 211 through 214' Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.809A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 4.264A pdb=" N VAL D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 322 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 375 through 386 removed outlier: 3.586A pdb=" N GLU D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 Processing helix chain 'D' and resid 477 through 497 removed outlier: 3.906A pdb=" N GLU D 481 " --> pdb=" O ASP D 478 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D 488 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP D 496 " --> pdb=" O ALA D 493 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 497 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.625A pdb=" N THR D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 529 Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.293A pdb=" N GLN D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 555 " --> pdb=" O TYR D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 577 Processing helix chain 'D' and resid 602 through 610 Processing helix chain 'D' and resid 671 through 673 No H-bonds generated for 'chain 'D' and resid 671 through 673' Processing helix chain 'D' and resid 677 through 689 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 715 through 725 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 68 through 86 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 103 through 129 removed outlier: 3.809A pdb=" N TRP F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 No H-bonds generated for 'chain 'F' and resid 134 through 137' Processing helix chain 'F' and resid 145 through 171 removed outlier: 4.774A pdb=" N ARG F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU F 161 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 205 removed outlier: 4.095A pdb=" N LYS F 192 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS F 193 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU F 196 " --> pdb=" O LYS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 4.043A pdb=" N SER F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE F 213 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 253 removed outlier: 4.391A pdb=" N ASP F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 268 Processing helix chain 'F' and resid 271 through 289 removed outlier: 4.054A pdb=" N ALA F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 317 Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 80 through 95 Processing helix chain 'C' and resid 108 through 114 removed outlier: 4.986A pdb=" N ASP C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.663A pdb=" N ASP C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 147 through 156 removed outlier: 4.042A pdb=" N GLN C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.721A pdb=" N PHE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 removed outlier: 4.167A pdb=" N LYS C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.808A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 322 removed outlier: 4.265A pdb=" N VAL C 320 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 375 through 386 removed outlier: 3.585A pdb=" N GLU C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 411 Processing helix chain 'C' and resid 477 through 497 removed outlier: 3.905A pdb=" N GLU C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL C 488 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP C 496 " --> pdb=" O ALA C 493 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 497 " --> pdb=" O LEU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.625A pdb=" N THR C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 529 Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.293A pdb=" N GLN C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 555 " --> pdb=" O TYR C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 602 through 610 Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 677 through 689 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 715 through 725 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 51 through 53 No H-bonds generated for 'chain 'H' and resid 51 through 53' Processing helix chain 'H' and resid 58 through 62 Processing helix chain 'H' and resid 68 through 86 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 103 through 129 removed outlier: 3.809A pdb=" N TRP H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN H 129 " --> pdb=" O HIS H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 137 No H-bonds generated for 'chain 'H' and resid 134 through 137' Processing helix chain 'H' and resid 145 through 171 removed outlier: 4.774A pdb=" N ARG H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR H 158 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU H 161 " --> pdb=" O TYR H 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE H 162 " --> pdb=" O TYR H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 205 removed outlier: 4.096A pdb=" N LYS H 192 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS H 193 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU H 196 " --> pdb=" O LYS H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 215 removed outlier: 4.043A pdb=" N SER H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA H 214 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 253 removed outlier: 4.391A pdb=" N ASP H 234 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 268 Processing helix chain 'H' and resid 271 through 289 removed outlier: 4.053A pdb=" N ALA H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 317 Processing helix chain 'H' and resid 336 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 228 through 231 removed outlier: 4.044A pdb=" N ILE A 230 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 338 through 341 removed outlier: 7.176A pdb=" N TYR A 415 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE A 341 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN A 417 " --> pdb=" O ILE A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 644 through 648 Processing sheet with id= D, first strand: chain 'B' and resid 228 through 231 removed outlier: 4.045A pdb=" N ILE B 230 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 338 through 341 removed outlier: 7.176A pdb=" N TYR B 415 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE B 341 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 417 " --> pdb=" O ILE B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 644 through 648 Processing sheet with id= G, first strand: chain 'D' and resid 228 through 231 removed outlier: 4.045A pdb=" N ILE D 230 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 338 through 341 removed outlier: 7.177A pdb=" N TYR D 415 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE D 341 " --> pdb=" O TYR D 415 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN D 417 " --> pdb=" O ILE D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 644 through 648 Processing sheet with id= J, first strand: chain 'C' and resid 228 through 231 removed outlier: 4.045A pdb=" N ILE C 230 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 338 through 341 removed outlier: 7.176A pdb=" N TYR C 415 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE C 341 " --> pdb=" O TYR C 415 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN C 417 " --> pdb=" O ILE C 341 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 644 through 648 1044 hydrogen bonds defined for protein. 2760 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: 8.69 Time building geometry restraints manager: 14.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9807 1.34 - 1.45: 4464 1.45 - 1.57: 16845 1.57 - 1.69: 52 1.69 - 1.81: 120 Bond restraints: 31288 Sorted by residual: bond pdb=" C3' CDP C 801 " pdb=" C4' CDP C 801 " ideal model delta sigma weight residual 1.305 1.517 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' CDP D 801 " pdb=" C4' CDP D 801 " ideal model delta sigma weight residual 1.305 1.517 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' CDP A 801 " pdb=" C4' CDP A 801 " ideal model delta sigma weight residual 1.305 1.517 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' CDP B 801 " pdb=" C4' CDP B 801 " ideal model delta sigma weight residual 1.305 1.517 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' CDP A 801 " pdb=" O4' CDP A 801 " ideal model delta sigma weight residual 1.615 1.429 0.186 2.00e-02 2.50e+03 8.64e+01 ... (remaining 31283 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 844 106.45 - 113.34: 16712 113.34 - 120.24: 11437 120.24 - 127.13: 13618 127.13 - 134.03: 325 Bond angle restraints: 42936 Sorted by residual: angle pdb=" PB DTP A 802 " pdb=" O3B DTP A 802 " pdb=" PG DTP A 802 " ideal model delta sigma weight residual 139.87 119.76 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP B 802 " pdb=" O3B DTP B 802 " pdb=" PG DTP B 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP C 802 " pdb=" O3B DTP C 802 " pdb=" PG DTP C 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP D 802 " pdb=" O3B DTP D 802 " pdb=" PG DTP D 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.03e+02 angle pdb=" PB DTP C 804 " pdb=" O3B DTP C 804 " pdb=" PG DTP C 804 " ideal model delta sigma weight residual 139.87 120.21 19.66 1.00e+00 1.00e+00 3.87e+02 ... (remaining 42931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 17836 34.45 - 68.90: 208 68.90 - 103.35: 24 103.35 - 137.80: 0 137.80 - 172.25: 4 Dihedral angle restraints: 18072 sinusoidal: 5316 harmonic: 12756 Sorted by residual: dihedral pdb=" O1B DTP B 802 " pdb=" O3B DTP B 802 " pdb=" PB DTP B 802 " pdb=" PG DTP B 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.18 -172.25 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1B DTP A 802 " pdb=" O3B DTP A 802 " pdb=" PB DTP A 802 " pdb=" PG DTP A 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.14 -172.21 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1B DTP C 802 " pdb=" O3B DTP C 802 " pdb=" PB DTP C 802 " pdb=" PG DTP C 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.11 -172.18 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 18069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4225 0.056 - 0.112: 659 0.112 - 0.168: 56 0.168 - 0.224: 8 0.224 - 0.281: 4 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C3' CDP D 801 " pdb=" C2' CDP D 801 " pdb=" C4' CDP D 801 " pdb=" O3' CDP D 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.67 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' CDP B 801 " pdb=" C2' CDP B 801 " pdb=" C4' CDP B 801 " pdb=" O3' CDP B 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.67 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3' CDP A 801 " pdb=" C2' CDP A 801 " pdb=" C4' CDP A 801 " pdb=" O3' CDP A 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.67 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 4949 not shown) Planarity restraints: 5564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 384 " -0.015 2.00e-02 2.50e+03 8.30e-03 1.38e+00 pdb=" CG TYR A 384 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 384 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 384 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 384 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 384 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 384 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 384 " 0.015 2.00e-02 2.50e+03 8.27e-03 1.37e+00 pdb=" CG TYR B 384 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 384 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 384 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 384 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 384 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 384 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 384 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 384 " 0.015 2.00e-02 2.50e+03 8.16e-03 1.33e+00 pdb=" CG TYR D 384 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 384 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 384 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 384 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 384 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 384 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 384 " 0.006 2.00e-02 2.50e+03 ... (remaining 5561 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 508 2.65 - 3.21: 30496 3.21 - 3.78: 45665 3.78 - 4.34: 57294 4.34 - 4.90: 89918 Nonbonded interactions: 223881 Sorted by model distance: nonbonded pdb=" O1G DTP A 802 " pdb="MG MG A 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP B 802 " pdb="MG MG B 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP C 802 " pdb="MG MG C 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP D 802 " pdb="MG MG D 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP A 804 " pdb="MG MG A 805 " model vdw 2.090 2.170 ... (remaining 223876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.740 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: 0.020 Extract box with map and model: 6.510 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 75.230 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.260 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.006 0.212 31288 Z= 0.416 Angle : 0.748 20.107 42936 Z= 0.545 Chirality : 0.041 0.281 4952 Planarity : 0.003 0.026 5564 Dihedral : 13.129 172.254 9872 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.75 % Favored : 89.15 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.11), residues: 4324 helix: -1.97 (0.10), residues: 1960 sheet: -3.01 (0.31), residues: 248 loop : -3.71 (0.11), residues: 2116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 420 time to evaluate : 3.855 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 424 average time/residue: 0.4028 time to fit residues: 281.3546 Evaluate side-chains 278 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 252 optimal weight: 0.5980 chunk 392 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 ASN G 242 HIS ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 31288 Z= 0.128 Angle : 0.486 5.608 42936 Z= 0.248 Chirality : 0.039 0.207 4952 Planarity : 0.003 0.040 5564 Dihedral : 7.028 167.979 4748 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.12), residues: 4324 helix: -0.93 (0.12), residues: 1948 sheet: -2.82 (0.30), residues: 252 loop : -3.32 (0.12), residues: 2124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3636 time to fit residues: 224.2422 Evaluate side-chains 279 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 0.3980 chunk 350 optimal weight: 9.9990 chunk 389 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 315 optimal weight: 3.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 632 ASN B 734 HIS G 247 GLN D 61 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN C 61 HIS ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 31288 Z= 0.288 Angle : 0.614 8.924 42936 Z= 0.319 Chirality : 0.042 0.170 4952 Planarity : 0.004 0.050 5564 Dihedral : 7.316 167.196 4748 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.97 % Favored : 86.96 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.12), residues: 4324 helix: -0.47 (0.12), residues: 1908 sheet: -2.64 (0.30), residues: 252 loop : -3.17 (0.12), residues: 2164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 344 time to evaluate : 3.633 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 345 average time/residue: 0.3697 time to fit residues: 216.3857 Evaluate side-chains 235 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2483 time to fit residues: 4.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 187 optimal weight: 0.4980 chunk 263 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 417 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 31288 Z= 0.127 Angle : 0.502 6.435 42936 Z= 0.255 Chirality : 0.039 0.154 4952 Planarity : 0.003 0.043 5564 Dihedral : 7.059 171.076 4748 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 4324 helix: -0.11 (0.12), residues: 1904 sheet: -2.29 (0.30), residues: 252 loop : -2.90 (0.12), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3776 time to fit residues: 229.0765 Evaluate side-chains 265 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 356 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 31288 Z= 0.200 Angle : 0.541 8.742 42936 Z= 0.277 Chirality : 0.040 0.228 4952 Planarity : 0.004 0.047 5564 Dihedral : 7.162 176.090 4748 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.45 % Favored : 88.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 4324 helix: -0.01 (0.12), residues: 1900 sheet: -2.17 (0.31), residues: 252 loop : -2.83 (0.12), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 3.549 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.3688 time to fit residues: 210.8500 Evaluate side-chains 255 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 417 optimal weight: 1.9990 chunk 346 optimal weight: 0.0370 chunk 193 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 31288 Z= 0.176 Angle : 0.522 6.718 42936 Z= 0.266 Chirality : 0.039 0.204 4952 Planarity : 0.003 0.038 5564 Dihedral : 7.220 178.908 4748 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4324 helix: 0.11 (0.12), residues: 1900 sheet: -1.94 (0.31), residues: 252 loop : -2.75 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.3716 time to fit residues: 209.1306 Evaluate side-chains 263 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 chunk 351 optimal weight: 0.1980 chunk 233 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN D 134 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 31288 Z= 0.124 Angle : 0.514 11.067 42936 Z= 0.256 Chirality : 0.039 0.182 4952 Planarity : 0.003 0.035 5564 Dihedral : 7.035 179.167 4748 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4324 helix: 0.27 (0.13), residues: 1884 sheet: -1.70 (0.31), residues: 252 loop : -2.65 (0.13), residues: 2188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3677 time to fit residues: 226.3201 Evaluate side-chains 266 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 0.0170 chunk 264 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 327 optimal weight: 10.0000 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 31288 Z= 0.140 Angle : 0.513 9.442 42936 Z= 0.255 Chirality : 0.039 0.242 4952 Planarity : 0.003 0.038 5564 Dihedral : 6.917 176.117 4748 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 4324 helix: 0.37 (0.13), residues: 1884 sheet: -1.47 (0.32), residues: 252 loop : -2.57 (0.13), residues: 2188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.3712 time to fit residues: 209.1674 Evaluate side-chains 268 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 9.9990 chunk 398 optimal weight: 0.6980 chunk 363 optimal weight: 3.9990 chunk 388 optimal weight: 0.0270 chunk 233 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 366 optimal weight: 0.4980 chunk 386 optimal weight: 10.0000 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 31288 Z= 0.178 Angle : 0.536 8.478 42936 Z= 0.269 Chirality : 0.039 0.171 4952 Planarity : 0.003 0.039 5564 Dihedral : 6.825 168.290 4748 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4324 helix: 0.35 (0.13), residues: 1880 sheet: -1.31 (0.34), residues: 232 loop : -2.50 (0.13), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.3868 time to fit residues: 216.4743 Evaluate side-chains 269 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 7.9990 chunk 410 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 430 optimal weight: 0.0170 chunk 396 optimal weight: 9.9990 chunk 342 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 31288 Z= 0.124 Angle : 0.522 8.164 42936 Z= 0.255 Chirality : 0.039 0.170 4952 Planarity : 0.003 0.035 5564 Dihedral : 6.518 161.302 4748 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4324 helix: 0.48 (0.13), residues: 1860 sheet: -1.08 (0.33), residues: 252 loop : -2.48 (0.13), residues: 2212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3736 time to fit residues: 218.2430 Evaluate side-chains 270 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 316 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 343 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: