Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:51:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/12_2022/7mlu_23910.pdb" } resolution = 4.1 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= -0.002 sd= 0.986 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21886 Number of models: 1 Model: "" Number of chains: 20 Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "O" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.48, per 1000 atoms: 0.57 Number of scatterers: 21886 At special positions: 0 Unit cell: (155.288, 153.636, 125.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 145 16.00 O 4048 8.00 N 3630 7.00 C 14063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 38 " Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 3.3 seconds 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 41 sheets defined 22.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.798A pdb=" N ASP K 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.150A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.118A pdb=" N SER G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.928A pdb=" N ASP O 82 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU O 83 " --> pdb=" O ALA O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 83' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.036A pdb=" N SER N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.948A pdb=" N LEU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 4.118A pdb=" N SER L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.100A pdb=" N LEU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.634A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.769A pdb=" N ILE A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.682A pdb=" N TRP A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 removed outlier: 3.770A pdb=" N ILE E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP E 243 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 269 removed outlier: 4.129A pdb=" N VAL E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.682A pdb=" N TRP E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET E 287 " --> pdb=" O ILE E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 removed outlier: 3.692A pdb=" N TYR E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 398 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 417 removed outlier: 3.548A pdb=" N ASN E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP E 414 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 415 " --> pdb=" O MET E 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR E 417 " --> pdb=" O TYR E 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 18 removed outlier: 3.634A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.768A pdb=" N ILE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.692A pdb=" N TRP D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE D 394 " --> pdb=" O ARG D 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 415 " --> pdb=" O MET D 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR D 417 " --> pdb=" O TYR D 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.770A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP B 243 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.548A pdb=" N ASN B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 226 removed outlier: 4.336A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.769A pdb=" N ILE C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP C 243 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.129A pdb=" N VAL C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 287 " --> pdb=" O ILE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.534A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.398A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'F' and resid 47 through 51 removed outlier: 6.555A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.365A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.592A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 34 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 19 through 21 removed outlier: 3.527A pdb=" N THR O 72 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 44 through 48 removed outlier: 6.425A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU O 85 " --> pdb=" O GLN O 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'N' and resid 47 through 51 removed outlier: 6.585A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE N 34 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.537A pdb=" N LEU M 73 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.496A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN M 38 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.602A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE L 34 " --> pdb=" O GLU L 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AB9, first strand: chain 'I' and resid 44 through 46 Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 47 through 51 removed outlier: 6.592A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN A 177 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 43 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET A 154 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 217 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET A 154 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLN E 177 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE E 43 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET E 154 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET E 154 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN D 177 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE D 43 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.974A pdb=" N MET D 154 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 217 " --> pdb=" O ILE D 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.974A pdb=" N MET D 154 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLN B 177 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 43 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN C 177 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE C 43 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET C 154 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 217 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET C 154 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2091 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: 7.35 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6813 1.34 - 1.46: 5653 1.46 - 1.58: 9722 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 22428 Sorted by residual: bond pdb=" C7 NAG D 501 " pdb=" N2 NAG D 501 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.10e-02 8.26e+03 5.91e+00 bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.63e+00 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.63e+00 bond pdb=" C7 NAG E 501 " pdb=" N2 NAG E 501 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.60e+00 bond pdb=" C7 NAG C 501 " pdb=" N2 NAG C 501 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.55e+00 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 99.96 - 107.28: 860 107.28 - 114.60: 12658 114.60 - 121.91: 11999 121.91 - 129.23: 4665 129.23 - 136.55: 216 Bond angle restraints: 30398 Sorted by residual: angle pdb=" C2 NAG A 501 " pdb=" N2 NAG A 501 " pdb=" C7 NAG A 501 " ideal model delta sigma weight residual 123.12 134.03 -10.91 1.28e+00 6.08e-01 7.24e+01 angle pdb=" C2 NAG E 501 " pdb=" N2 NAG E 501 " pdb=" C7 NAG E 501 " ideal model delta sigma weight residual 123.12 134.03 -10.91 1.28e+00 6.08e-01 7.24e+01 angle pdb=" C2 NAG B 501 " pdb=" N2 NAG B 501 " pdb=" C7 NAG B 501 " ideal model delta sigma weight residual 123.12 134.02 -10.90 1.28e+00 6.08e-01 7.22e+01 angle pdb=" C2 NAG D 501 " pdb=" N2 NAG D 501 " pdb=" C7 NAG D 501 " ideal model delta sigma weight residual 123.12 134.00 -10.88 1.28e+00 6.08e-01 7.19e+01 angle pdb=" C2 NAG C 501 " pdb=" N2 NAG C 501 " pdb=" C7 NAG C 501 " ideal model delta sigma weight residual 123.12 133.99 -10.87 1.28e+00 6.08e-01 7.18e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 12534 14.39 - 28.78: 563 28.78 - 43.17: 128 43.17 - 57.56: 17 57.56 - 71.95: 17 Dihedral angle restraints: 13259 sinusoidal: 5284 harmonic: 7975 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 28.34 64.66 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 32.55 60.45 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.77 45.23 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 13256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2876 0.076 - 0.151: 438 0.151 - 0.227: 39 0.227 - 0.303: 0 0.303 - 0.379: 5 Chirality restraints: 3358 Sorted by residual: chirality pdb=" C2 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C3 NAG D 501 " pdb=" N2 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C2 NAG C 501 " pdb=" C1 NAG C 501 " pdb=" C3 NAG C 501 " pdb=" N2 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 3355 not shown) Planarity restraints: 3813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 58 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO K 59 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO K 59 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 59 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 86 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO D 87 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO E 87 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " 0.029 5.00e-02 4.00e+02 ... (remaining 3810 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5580 2.80 - 3.32: 18770 3.32 - 3.85: 36511 3.85 - 4.37: 42175 4.37 - 4.90: 69745 Nonbonded interactions: 172781 Sorted by model distance: nonbonded pdb=" OG1 THR D 162 " pdb=" OD1 ASN D 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR E 162 " pdb=" OD1 ASN E 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR C 162 " pdb=" OD1 ASN C 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR A 162 " pdb=" OD1 ASN A 164 " model vdw 2.271 2.440 ... (remaining 172776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'I' and resid 2 through 102) selection = chain 'J' selection = (chain 'K' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) selection = (chain 'M' and resid 2 through 102) selection = (chain 'O' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 145 5.16 5 C 14063 2.51 5 N 3630 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.450 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: 15.470 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.190 Process input model: 59.290 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 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 : 0.004 0.052 22428 Z= 0.259 Angle : 0.877 15.737 30398 Z= 0.483 Chirality : 0.053 0.379 3358 Planarity : 0.006 0.056 3808 Dihedral : 9.468 71.951 8087 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.21 % 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: -4.41 (0.13), residues: 2706 helix: -3.90 (0.13), residues: 380 sheet: -2.50 (0.17), residues: 675 loop : -2.99 (0.12), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 590 time to evaluate : 2.750 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 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: 5 outliers final: 0 residues processed: 595 average time/residue: 0.3589 time to fit residues: 316.1884 Evaluate side-chains 323 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 5.9990 chunk 204 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 HIS K 37 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 115 ASN A 125 ASN A 155 GLN A 164 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN E 61 ASN E 67 GLN E 115 ASN E 125 ASN E 186 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN D 61 ASN D 67 GLN D 125 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 305 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 125 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 115 ASN C 125 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 226 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22428 Z= 0.169 Angle : 0.651 14.204 30398 Z= 0.336 Chirality : 0.043 0.183 3358 Planarity : 0.005 0.048 3808 Dihedral : 5.564 27.230 3008 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.08 % 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: -3.21 (0.14), residues: 2706 helix: -2.36 (0.19), residues: 455 sheet: -1.78 (0.17), residues: 737 loop : -2.25 (0.15), residues: 1514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 2.635 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 revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 432 average time/residue: 0.3419 time to fit residues: 226.3891 Evaluate side-chains 308 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN N 43 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN I 38 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 305 ASN E 107 HIS ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 22428 Z= 0.353 Angle : 0.830 16.025 30398 Z= 0.433 Chirality : 0.047 0.287 3358 Planarity : 0.005 0.047 3808 Dihedral : 6.180 24.981 3008 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.72 % Favored : 91.24 % 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: -2.76 (0.15), residues: 2706 helix: -1.35 (0.22), residues: 460 sheet: -1.84 (0.18), residues: 734 loop : -1.99 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 2.789 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 outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.3456 time to fit residues: 186.9171 Evaluate side-chains 265 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 117 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 233 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 305 ASN E 305 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 22428 Z= 0.321 Angle : 0.779 16.939 30398 Z= 0.398 Chirality : 0.046 0.284 3358 Planarity : 0.005 0.058 3808 Dihedral : 6.209 24.261 3008 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 30.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % 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: -2.49 (0.16), residues: 2706 helix: -0.96 (0.23), residues: 460 sheet: -1.67 (0.18), residues: 769 loop : -1.85 (0.16), residues: 1477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 2.789 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 outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.3350 time to fit residues: 165.6538 Evaluate side-chains 250 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.0030 chunk 222 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 HIS ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 177 GLN B 46 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 22428 Z= 0.269 Angle : 0.726 16.626 30398 Z= 0.367 Chirality : 0.044 0.194 3358 Planarity : 0.004 0.047 3808 Dihedral : 5.973 23.139 3008 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % 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: -2.25 (0.16), residues: 2706 helix: -0.69 (0.25), residues: 420 sheet: -1.62 (0.18), residues: 766 loop : -1.63 (0.16), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.755 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 outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.3451 time to fit residues: 166.4636 Evaluate side-chains 245 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 HIS A 31 ASN A 46 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 22428 Z= 0.334 Angle : 0.796 16.249 30398 Z= 0.408 Chirality : 0.046 0.350 3358 Planarity : 0.005 0.059 3808 Dihedral : 6.326 25.909 3008 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 35.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % 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: -2.47 (0.16), residues: 2706 helix: -0.82 (0.24), residues: 420 sheet: -1.88 (0.18), residues: 768 loop : -1.72 (0.16), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.560 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 outliers start: 1 outliers final: 1 residues processed: 289 average time/residue: 0.3403 time to fit residues: 152.2992 Evaluate side-chains 227 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1982 time to fit residues: 3.9194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 260 optimal weight: 0.0770 chunk 162 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.8959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 22428 Z= 0.252 Angle : 0.725 16.051 30398 Z= 0.368 Chirality : 0.045 0.199 3358 Planarity : 0.005 0.078 3808 Dihedral : 6.083 27.481 3008 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % 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: -2.32 (0.16), residues: 2706 helix: -0.44 (0.25), residues: 390 sheet: -1.81 (0.17), residues: 788 loop : -1.67 (0.16), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.532 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 outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.3323 time to fit residues: 153.0102 Evaluate side-chains 233 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.9144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 22428 Z= 0.192 Angle : 0.693 14.391 30398 Z= 0.350 Chirality : 0.045 0.200 3358 Planarity : 0.004 0.060 3808 Dihedral : 5.791 23.772 3008 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % 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: -2.01 (0.16), residues: 2706 helix: -0.10 (0.27), residues: 380 sheet: -1.61 (0.18), residues: 741 loop : -1.50 (0.16), residues: 1585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.666 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 outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3331 time to fit residues: 155.7941 Evaluate side-chains 238 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 227 optimal weight: 0.0980 chunk 242 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 219 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 22428 Z= 0.279 Angle : 0.753 18.566 30398 Z= 0.382 Chirality : 0.045 0.192 3358 Planarity : 0.005 0.043 3808 Dihedral : 6.021 23.617 3008 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % 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: -2.09 (0.16), residues: 2706 helix: -0.27 (0.26), residues: 380 sheet: -1.63 (0.18), residues: 693 loop : -1.57 (0.16), residues: 1633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 2.834 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 outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.3297 time to fit residues: 147.7480 Evaluate side-chains 227 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.9762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 22428 Z= 0.207 Angle : 0.709 18.432 30398 Z= 0.356 Chirality : 0.045 0.198 3358 Planarity : 0.004 0.040 3808 Dihedral : 5.793 22.360 3008 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -1.91 (0.16), residues: 2706 helix: -0.02 (0.27), residues: 380 sheet: -1.49 (0.19), residues: 698 loop : -1.48 (0.16), residues: 1628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.780 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 outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3290 time to fit residues: 152.3221 Evaluate side-chains 233 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3096 > 50: distance: 37 - 39: 20.265 distance: 39 - 40: 7.557 distance: 40 - 41: 23.954 distance: 40 - 43: 20.724 distance: 41 - 42: 25.401 distance: 41 - 50: 22.283 distance: 43 - 44: 13.108 distance: 44 - 45: 8.681 distance: 45 - 46: 9.047 distance: 46 - 47: 6.462 distance: 47 - 48: 7.750 distance: 47 - 49: 4.275 distance: 50 - 51: 7.276 distance: 51 - 52: 7.146 distance: 51 - 54: 8.613 distance: 52 - 53: 3.125 distance: 54 - 55: 8.842 distance: 55 - 56: 18.674 distance: 55 - 57: 14.175 distance: 56 - 58: 21.409 distance: 57 - 59: 22.266 distance: 58 - 60: 15.053 distance: 59 - 60: 13.937 distance: 61 - 62: 19.079 distance: 61 - 136: 8.705 distance: 62 - 63: 23.551 distance: 62 - 65: 15.625 distance: 63 - 64: 10.219 distance: 63 - 68: 10.037 distance: 64 - 133: 29.507 distance: 65 - 66: 26.046 distance: 65 - 67: 18.115 distance: 68 - 69: 7.522 distance: 69 - 70: 18.248 distance: 70 - 71: 9.790 distance: 70 - 72: 25.472 distance: 72 - 122: 26.698 distance: 73 - 74: 10.087 distance: 73 - 76: 18.080 distance: 74 - 75: 8.990 distance: 74 - 78: 21.469 distance: 75 - 119: 25.934 distance: 76 - 77: 7.303 distance: 78 - 79: 28.643 distance: 79 - 80: 39.340 distance: 82 - 83: 6.061 distance: 83 - 84: 4.729 distance: 83 - 86: 52.628 distance: 84 - 88: 4.094 distance: 86 - 87: 36.726 distance: 89 - 90: 18.746 distance: 90 - 91: 24.367 distance: 90 - 92: 11.831 distance: 92 - 93: 4.253 distance: 93 - 94: 6.468 distance: 94 - 95: 8.275 distance: 94 - 99: 12.198 distance: 96 - 98: 8.941 distance: 99 - 100: 16.481 distance: 100 - 101: 6.563 distance: 100 - 103: 32.013 distance: 101 - 102: 11.648 distance: 101 - 107: 21.477 distance: 104 - 105: 22.530 distance: 104 - 106: 10.446