Starting phenix.real_space_refine on Thu Aug 8 04:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/08_2024/7mlu_23910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/08_2024/7mlu_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_23910/08_2024/7mlu_23910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/08_2024/7mlu_23910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/08_2024/7mlu_23910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/08_2024/7mlu_23910.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.33, per 1000 atoms: 0.56 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: 7.59 Conformation dependent library (CDL) restraints added in 4.1 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: 3.06 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: 7.38 Time building geometry restraints manager: 8.48 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=" C THR K 94 " pdb=" N PRO K 95 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.90e+00 bond pdb=" C THR J 94 " pdb=" N PRO J 95 " ideal model delta sigma weight residual 1.334 1.385 -0.052 2.34e-02 1.83e+03 4.85e+00 bond pdb=" C THR O 94 " pdb=" N PRO O 95 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.75e+00 bond pdb=" C THR I 94 " pdb=" N PRO I 95 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.40e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.99e+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=" N GLY B 205 " pdb=" CA GLY B 205 " pdb=" C GLY B 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY C 205 " pdb=" CA GLY C 205 " pdb=" C GLY C 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY D 205 " pdb=" CA GLY D 205 " pdb=" C GLY D 205 " ideal model delta sigma weight residual 110.29 117.02 -6.73 1.28e+00 6.10e-01 2.77e+01 angle pdb=" N GLY E 205 " pdb=" CA GLY E 205 " pdb=" C GLY E 205 " ideal model delta sigma weight residual 110.29 117.02 -6.73 1.28e+00 6.10e-01 2.76e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 12589 14.39 - 28.78: 563 28.78 - 43.17: 128 43.17 - 57.56: 27 57.56 - 71.95: 27 Dihedral angle restraints: 13334 sinusoidal: 5359 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 13331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2872 0.076 - 0.152: 443 0.152 - 0.227: 38 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 3.59e+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 3.59e+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 3.55e+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 3.040 nonbonded pdb=" OG1 THR E 162 " pdb=" OD1 ASN E 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR C 162 " pdb=" OD1 ASN C 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 162 " pdb=" OD1 ASN A 164 " model vdw 2.271 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 4.920 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: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 57.920 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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= 0.265 Angle : 0.879 15.737 30398 Z= 0.464 Chirality : 0.054 0.379 3358 Planarity : 0.006 0.056 3808 Dihedral : 9.815 71.951 8162 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.21 % Allowed : 2.77 % Favored : 97.02 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 94 HIS 0.006 0.001 HIS M 91 PHE 0.022 0.002 PHE D 63 TYR 0.021 0.002 TYR I 49 ARG 0.011 0.001 ARG C 29 *********************** 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 : 2.563 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 REVERT: K 78 VAL cc_start: 0.8066 (t) cc_final: 0.6732 (t) REVERT: F 45 LEU cc_start: 0.7573 (mm) cc_final: 0.6899 (mm) REVERT: F 114 LEU cc_start: 0.8669 (tp) cc_final: 0.8007 (mm) REVERT: J 4 MET cc_start: 0.5939 (mmm) cc_final: 0.5739 (mmp) REVERT: G 12 MET cc_start: 0.8886 (mmt) cc_final: 0.8622 (tpp) REVERT: G 71 THR cc_start: 0.7931 (p) cc_final: 0.7679 (p) REVERT: G 83 LEU cc_start: 0.9030 (mt) cc_final: 0.8777 (pp) REVERT: O 20 SER cc_start: 0.8021 (m) cc_final: 0.7506 (p) REVERT: O 50 TRP cc_start: 0.7264 (m100) cc_final: 0.7057 (m100) REVERT: N 45 LEU cc_start: 0.7507 (mm) cc_final: 0.7067 (tp) REVERT: N 77 ASN cc_start: 0.8260 (m-40) cc_final: 0.7912 (p0) REVERT: N 95 TYR cc_start: 0.7068 (m-80) cc_final: 0.6624 (m-80) REVERT: N 114 LEU cc_start: 0.9074 (tp) cc_final: 0.8615 (mm) REVERT: M 78 VAL cc_start: 0.7580 (t) cc_final: 0.6925 (t) REVERT: L 103 ASN cc_start: 0.7453 (m-40) cc_final: 0.7134 (m-40) REVERT: I 2 ILE cc_start: 0.8314 (mt) cc_final: 0.7304 (mt) REVERT: I 4 MET cc_start: 0.7880 (mmm) cc_final: 0.7561 (mmm) REVERT: H 106 ASP cc_start: 0.8208 (p0) cc_final: 0.7928 (p0) REVERT: A 246 MET cc_start: 0.3527 (ptt) cc_final: 0.2978 (ptm) REVERT: A 287 MET cc_start: 0.8925 (mmm) cc_final: 0.8613 (ttp) REVERT: A 404 MET cc_start: 0.9189 (mmm) cc_final: 0.8925 (mmp) REVERT: E 404 MET cc_start: 0.8835 (mmm) cc_final: 0.8576 (mmt) REVERT: D 227 MET cc_start: 0.7951 (mmp) cc_final: 0.7071 (mmm) REVERT: D 233 LEU cc_start: 0.8807 (tp) cc_final: 0.8558 (tt) REVERT: D 246 MET cc_start: 0.6965 (ptt) cc_final: 0.6670 (ttm) REVERT: D 263 MET cc_start: 0.8700 (mmm) cc_final: 0.8046 (mmt) REVERT: D 404 MET cc_start: 0.8426 (mmm) cc_final: 0.8211 (mtt) REVERT: B 62 ILE cc_start: 0.8969 (pt) cc_final: 0.8417 (pt) REVERT: B 246 MET cc_start: 0.4050 (ptt) cc_final: 0.3328 (ppp) REVERT: B 263 MET cc_start: 0.8678 (mmm) cc_final: 0.8276 (tpt) REVERT: B 404 MET cc_start: 0.8645 (mmm) cc_final: 0.8186 (mtt) REVERT: C 246 MET cc_start: 0.6158 (ptt) cc_final: 0.5366 (ppp) REVERT: C 404 MET cc_start: 0.8093 (mmm) cc_final: 0.7665 (mtt) outliers start: 5 outliers final: 0 residues processed: 595 average time/residue: 0.3825 time to fit residues: 339.3782 Evaluate side-chains 329 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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: 10.0000 chunk 204 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.0670 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 overall best weight: 3.7924 ------------------------------------------------------------------------------- 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 5 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** ** G 82 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** N 43 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS 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 226 GLN A 305 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 115 ASN E 125 ASN ** E 186 GLN ** 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 125 ASN D 155 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN 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 226 GLN B 305 ASN C 67 GLN C 115 ASN C 125 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 226 GLN C 305 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22428 Z= 0.269 Angle : 0.741 16.222 30398 Z= 0.376 Chirality : 0.045 0.247 3358 Planarity : 0.005 0.073 3808 Dihedral : 6.869 58.888 3083 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.85 % 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: -3.07 (0.15), residues: 2706 helix: -1.86 (0.22), residues: 420 sheet: -1.88 (0.17), residues: 695 loop : -2.20 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 94 HIS 0.006 0.001 HIS O 55 PHE 0.024 0.002 PHE A 99 TYR 0.021 0.002 TYR O 49 ARG 0.007 0.001 ARG E 131 *********************** 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 408 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 406 time to evaluate : 2.309 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: K 11 MET cc_start: 0.5829 (mmm) cc_final: 0.5490 (mmm) REVERT: F 114 LEU cc_start: 0.8839 (tp) cc_final: 0.8516 (mm) REVERT: J 4 MET cc_start: 0.6610 (mmm) cc_final: 0.6409 (mmp) REVERT: G 12 MET cc_start: 0.8735 (mmt) cc_final: 0.8287 (mmm) REVERT: G 73 GLU cc_start: 0.8695 (tt0) cc_final: 0.8128 (tt0) REVERT: G 83 LEU cc_start: 0.9121 (mt) cc_final: 0.8791 (pp) REVERT: O 11 MET cc_start: 0.5511 (mmm) cc_final: 0.5289 (mmm) REVERT: O 49 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6223 (p90) REVERT: N 45 LEU cc_start: 0.7543 (mm) cc_final: 0.7266 (tp) REVERT: N 63 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8251 (mmmm) REVERT: N 81 MET cc_start: 0.8056 (ttm) cc_final: 0.7594 (tmm) REVERT: N 114 LEU cc_start: 0.9173 (tp) cc_final: 0.8920 (mm) REVERT: L 11 LEU cc_start: 0.9057 (tp) cc_final: 0.8344 (tp) REVERT: L 12 MET cc_start: 0.8157 (mmm) cc_final: 0.7862 (mmm) REVERT: L 83 LEU cc_start: 0.8844 (mt) cc_final: 0.8504 (mp) REVERT: L 103 ASN cc_start: 0.7849 (m-40) cc_final: 0.7616 (t0) REVERT: I 2 ILE cc_start: 0.8114 (mt) cc_final: 0.7310 (mt) REVERT: I 4 MET cc_start: 0.8117 (mmm) cc_final: 0.7459 (mmm) REVERT: I 86 TYR cc_start: 0.7716 (m-10) cc_final: 0.7404 (m-10) REVERT: H 83 LEU cc_start: 0.9356 (mm) cc_final: 0.9065 (pp) REVERT: A 140 MET cc_start: 0.7923 (mtm) cc_final: 0.6761 (mtm) REVERT: A 246 MET cc_start: 0.3648 (ptt) cc_final: 0.3121 (ptm) REVERT: A 264 THR cc_start: 0.9149 (m) cc_final: 0.8874 (p) REVERT: A 287 MET cc_start: 0.9087 (mmm) cc_final: 0.8653 (tpt) REVERT: A 291 LEU cc_start: 0.9349 (mp) cc_final: 0.8649 (mp) REVERT: A 404 MET cc_start: 0.9189 (mmm) cc_final: 0.8921 (mmp) REVERT: E 32 PHE cc_start: 0.8060 (p90) cc_final: 0.7843 (p90) REVERT: E 140 MET cc_start: 0.8231 (mtm) cc_final: 0.6617 (mtm) REVERT: E 404 MET cc_start: 0.8822 (mmm) cc_final: 0.8553 (mmt) REVERT: E 411 MET cc_start: 0.9010 (ptp) cc_final: 0.8748 (ppp) REVERT: D 227 MET cc_start: 0.7898 (mmp) cc_final: 0.7642 (mmm) REVERT: D 246 MET cc_start: 0.7029 (ptt) cc_final: 0.6696 (ttm) REVERT: D 263 MET cc_start: 0.8727 (mmm) cc_final: 0.8031 (mmt) REVERT: D 404 MET cc_start: 0.8614 (mmm) cc_final: 0.8310 (mtt) REVERT: B 246 MET cc_start: 0.4368 (ptt) cc_final: 0.3583 (ppp) REVERT: B 261 LEU cc_start: 0.9373 (tt) cc_final: 0.9135 (pp) REVERT: B 404 MET cc_start: 0.8725 (mmm) cc_final: 0.8265 (mtt) REVERT: C 246 MET cc_start: 0.6211 (ptt) cc_final: 0.5534 (ppp) REVERT: C 263 MET cc_start: 0.8709 (mmt) cc_final: 0.7677 (mmt) REVERT: C 404 MET cc_start: 0.8317 (mmm) cc_final: 0.7755 (mtt) outliers start: 2 outliers final: 0 residues processed: 408 average time/residue: 0.3285 time to fit residues: 205.1763 Evaluate side-chains 302 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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: 9.9990 chunk 76 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 5 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** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 89 GLN L 3 GLN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 107 HIS ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN B 46 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 22428 Z= 0.432 Angle : 0.930 17.973 30398 Z= 0.472 Chirality : 0.050 0.258 3358 Planarity : 0.007 0.092 3808 Dihedral : 7.633 58.166 3083 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.89 % 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: -2.97 (0.15), residues: 2706 helix: -1.54 (0.23), residues: 395 sheet: -2.16 (0.17), residues: 772 loop : -1.98 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP C 94 HIS 0.010 0.002 HIS M 91 PHE 0.022 0.003 PHE E 99 TYR 0.038 0.003 TYR F 80 ARG 0.035 0.001 ARG M 18 *********************** 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 327 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 2.352 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: J 9 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8339 (mmtm) REVERT: J 62 PHE cc_start: 0.8527 (m-80) cc_final: 0.8173 (m-80) REVERT: G 12 MET cc_start: 0.8897 (mmt) cc_final: 0.8371 (mmm) REVERT: N 12 MET cc_start: 0.7178 (tpt) cc_final: 0.6447 (tpp) REVERT: N 114 LEU cc_start: 0.9336 (tp) cc_final: 0.8911 (tp) REVERT: I 4 MET cc_start: 0.7749 (mmm) cc_final: 0.7156 (mmm) REVERT: I 11 MET cc_start: 0.7092 (mmm) cc_final: 0.6880 (mmm) REVERT: I 86 TYR cc_start: 0.8005 (m-10) cc_final: 0.7548 (m-80) REVERT: H 20 ILE cc_start: 0.5521 (pt) cc_final: 0.5183 (pt) REVERT: A 43 ILE cc_start: 0.9419 (pt) cc_final: 0.8951 (mm) REVERT: A 246 MET cc_start: 0.3854 (ptt) cc_final: 0.3405 (ptm) REVERT: A 263 MET cc_start: 0.8986 (mmp) cc_final: 0.8594 (mmm) REVERT: A 264 THR cc_start: 0.9405 (m) cc_final: 0.9105 (p) REVERT: A 404 MET cc_start: 0.9145 (mmm) cc_final: 0.8865 (mmp) REVERT: E 56 MET cc_start: 0.9285 (tpp) cc_final: 0.8994 (tpp) REVERT: E 147 MET cc_start: 0.8401 (ttp) cc_final: 0.8198 (ttt) REVERT: E 287 MET cc_start: 0.9267 (ttm) cc_final: 0.9027 (ttm) REVERT: E 404 MET cc_start: 0.9012 (mmm) cc_final: 0.8734 (mmt) REVERT: E 411 MET cc_start: 0.9127 (ptp) cc_final: 0.8857 (ppp) REVERT: D 56 MET cc_start: 0.9150 (ttm) cc_final: 0.8143 (tpp) REVERT: D 140 MET cc_start: 0.7735 (mtm) cc_final: 0.6464 (mtm) REVERT: D 227 MET cc_start: 0.8810 (mmp) cc_final: 0.8356 (mmm) REVERT: D 263 MET cc_start: 0.9119 (mmm) cc_final: 0.8368 (mmt) REVERT: D 404 MET cc_start: 0.8818 (mmm) cc_final: 0.8475 (mtt) REVERT: B 147 MET cc_start: 0.8181 (ptm) cc_final: 0.7976 (ptm) REVERT: B 220 MET cc_start: 0.8133 (mmm) cc_final: 0.7707 (tpp) REVERT: B 246 MET cc_start: 0.4971 (ptt) cc_final: 0.4281 (ppp) REVERT: B 404 MET cc_start: 0.8826 (mmm) cc_final: 0.8427 (mtt) REVERT: C 246 MET cc_start: 0.6530 (ptt) cc_final: 0.5832 (ppp) REVERT: C 263 MET cc_start: 0.9051 (mmt) cc_final: 0.7958 (mmt) REVERT: C 404 MET cc_start: 0.8538 (mmm) cc_final: 0.8091 (mtt) outliers start: 3 outliers final: 0 residues processed: 327 average time/residue: 0.3242 time to fit residues: 163.4291 Evaluate side-chains 246 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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: 9.9990 chunk 184 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 70 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: ** J 38 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 91 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN E 46 ASN E 177 GLN ** E 186 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN B 46 ASN B 186 GLN C 46 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.7379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 22428 Z= 0.298 Angle : 0.772 17.476 30398 Z= 0.384 Chirality : 0.046 0.230 3358 Planarity : 0.005 0.069 3808 Dihedral : 7.132 57.317 3083 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % 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: -2.63 (0.15), residues: 2706 helix: -1.12 (0.24), residues: 395 sheet: -1.90 (0.18), residues: 734 loop : -1.84 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 239 HIS 0.008 0.002 HIS D 201 PHE 0.016 0.002 PHE C 100 TYR 0.029 0.002 TYR I 49 ARG 0.011 0.001 ARG K 54 *********************** 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 316 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 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 REVERT: F 81 MET cc_start: 0.8664 (tmm) cc_final: 0.8317 (tmm) REVERT: J 9 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8352 (mmtm) REVERT: G 81 MET cc_start: 0.7939 (tpt) cc_final: 0.7656 (tpt) REVERT: O 92 TYR cc_start: 0.8059 (t80) cc_final: 0.7827 (t80) REVERT: N 37 LEU cc_start: 0.8555 (mp) cc_final: 0.7964 (tt) REVERT: N 45 LEU cc_start: 0.7803 (tp) cc_final: 0.6673 (tp) REVERT: N 52 LEU cc_start: 0.9123 (mt) cc_final: 0.8666 (mt) REVERT: N 81 MET cc_start: 0.8828 (tmm) cc_final: 0.8595 (tmm) REVERT: N 114 LEU cc_start: 0.9328 (tp) cc_final: 0.9037 (tp) REVERT: L 80 TYR cc_start: 0.6353 (m-80) cc_final: 0.5950 (m-80) REVERT: I 4 MET cc_start: 0.7844 (mmm) cc_final: 0.7285 (mmm) REVERT: I 86 TYR cc_start: 0.8131 (m-10) cc_final: 0.7547 (m-10) REVERT: A 147 MET cc_start: 0.8922 (mmp) cc_final: 0.8666 (tpp) REVERT: A 246 MET cc_start: 0.4145 (ptt) cc_final: 0.3683 (ptm) REVERT: A 264 THR cc_start: 0.9395 (m) cc_final: 0.9069 (p) REVERT: A 404 MET cc_start: 0.9167 (mmm) cc_final: 0.8896 (mmp) REVERT: E 56 MET cc_start: 0.9184 (tpp) cc_final: 0.8556 (tpp) REVERT: E 147 MET cc_start: 0.8498 (ttp) cc_final: 0.8259 (ttp) REVERT: E 157 GLU cc_start: 0.9122 (pt0) cc_final: 0.8842 (pt0) REVERT: E 287 MET cc_start: 0.9321 (ttm) cc_final: 0.9079 (ttm) REVERT: E 404 MET cc_start: 0.9082 (mmm) cc_final: 0.8722 (mmt) REVERT: E 411 MET cc_start: 0.9043 (ptp) cc_final: 0.8799 (ppp) REVERT: D 56 MET cc_start: 0.9139 (ttm) cc_final: 0.7857 (tpp) REVERT: D 140 MET cc_start: 0.7816 (mtm) cc_final: 0.6259 (mtm) REVERT: D 263 MET cc_start: 0.9171 (mmm) cc_final: 0.8383 (mmt) REVERT: D 404 MET cc_start: 0.8881 (mmm) cc_final: 0.8523 (mtt) REVERT: B 246 MET cc_start: 0.5095 (ptt) cc_final: 0.4468 (ppp) REVERT: B 404 MET cc_start: 0.8839 (mmm) cc_final: 0.8435 (mtt) REVERT: C 56 MET cc_start: 0.9245 (tpp) cc_final: 0.8747 (tpp) REVERT: C 246 MET cc_start: 0.6657 (ptt) cc_final: 0.5959 (ppp) REVERT: C 263 MET cc_start: 0.9023 (mmt) cc_final: 0.8105 (mmt) REVERT: C 404 MET cc_start: 0.8587 (mmm) cc_final: 0.8121 (mtt) outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 0.3370 time to fit residues: 164.4798 Evaluate side-chains 248 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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: 0.0570 chunk 148 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 overall best weight: 3.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 HIS ** 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 186 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.7748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22428 Z= 0.214 Angle : 0.713 15.446 30398 Z= 0.353 Chirality : 0.045 0.227 3358 Planarity : 0.004 0.046 3808 Dihedral : 6.695 56.350 3083 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -2.39 (0.16), residues: 2706 helix: -0.84 (0.24), residues: 425 sheet: -1.76 (0.18), residues: 753 loop : -1.69 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 239 HIS 0.007 0.001 HIS D 201 PHE 0.015 0.002 PHE E 409 TYR 0.021 0.002 TYR M 49 ARG 0.008 0.001 ARG K 54 *********************** 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 314 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 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 REVERT: K 10 PHE cc_start: 0.7853 (t80) cc_final: 0.7371 (t80) REVERT: J 9 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8408 (mmtm) REVERT: J 62 PHE cc_start: 0.8405 (m-80) cc_final: 0.8074 (m-80) REVERT: G 12 MET cc_start: 0.8342 (mmp) cc_final: 0.7457 (mmm) REVERT: N 37 LEU cc_start: 0.8495 (mp) cc_final: 0.7946 (tt) REVERT: N 45 LEU cc_start: 0.7849 (tp) cc_final: 0.6584 (tp) REVERT: N 52 LEU cc_start: 0.9033 (mt) cc_final: 0.8528 (mt) REVERT: N 81 MET cc_start: 0.8832 (tmm) cc_final: 0.8599 (tmm) REVERT: N 114 LEU cc_start: 0.9294 (tp) cc_final: 0.8911 (tp) REVERT: L 12 MET cc_start: 0.8053 (mmp) cc_final: 0.7767 (mmm) REVERT: L 19 LYS cc_start: 0.8594 (pptt) cc_final: 0.8349 (tmmt) REVERT: L 69 THR cc_start: 0.8922 (m) cc_final: 0.8427 (m) REVERT: L 80 TYR cc_start: 0.6372 (m-80) cc_final: 0.6170 (m-80) REVERT: I 4 MET cc_start: 0.7872 (mmm) cc_final: 0.7319 (mmm) REVERT: I 11 MET cc_start: 0.7472 (mmm) cc_final: 0.7119 (mmm) REVERT: I 86 TYR cc_start: 0.8157 (m-10) cc_final: 0.7650 (m-10) REVERT: H 81 MET cc_start: 0.7940 (mtm) cc_final: 0.7707 (mtm) REVERT: A 246 MET cc_start: 0.4301 (ptt) cc_final: 0.3772 (ptm) REVERT: A 263 MET cc_start: 0.8990 (mmp) cc_final: 0.8590 (mmm) REVERT: A 264 THR cc_start: 0.9378 (m) cc_final: 0.9097 (p) REVERT: A 287 MET cc_start: 0.8795 (tmm) cc_final: 0.8321 (tpp) REVERT: A 404 MET cc_start: 0.9193 (mmm) cc_final: 0.8936 (mmp) REVERT: E 147 MET cc_start: 0.8518 (ttp) cc_final: 0.8213 (ttt) REVERT: E 157 GLU cc_start: 0.8956 (pt0) cc_final: 0.8722 (pt0) REVERT: E 163 MET cc_start: 0.8541 (mmm) cc_final: 0.8044 (mmm) REVERT: E 287 MET cc_start: 0.9303 (ttm) cc_final: 0.9094 (ttm) REVERT: E 404 MET cc_start: 0.9174 (mmm) cc_final: 0.8903 (mmt) REVERT: E 411 MET cc_start: 0.8983 (ptp) cc_final: 0.8742 (ppp) REVERT: D 56 MET cc_start: 0.9038 (ttm) cc_final: 0.8616 (tpp) REVERT: D 147 MET cc_start: 0.9048 (pmm) cc_final: 0.8827 (pmm) REVERT: D 263 MET cc_start: 0.9144 (mmm) cc_final: 0.8378 (mmt) REVERT: D 404 MET cc_start: 0.8975 (mmm) cc_final: 0.8611 (mtt) REVERT: B 246 MET cc_start: 0.5209 (ptt) cc_final: 0.4601 (ppp) REVERT: B 404 MET cc_start: 0.8848 (mmm) cc_final: 0.8445 (mtt) REVERT: C 246 MET cc_start: 0.6658 (ptt) cc_final: 0.5998 (ppp) REVERT: C 404 MET cc_start: 0.8574 (mmm) cc_final: 0.8076 (mtt) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.3289 time to fit residues: 160.8004 Evaluate side-chains 256 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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: 8.9990 chunk 235 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 0.0050 chunk 261 optimal weight: 30.0000 chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 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** A 46 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 46 ASN ** E 186 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 115 ASN B 46 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.8610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22428 Z= 0.317 Angle : 0.793 15.194 30398 Z= 0.395 Chirality : 0.046 0.230 3358 Planarity : 0.005 0.089 3808 Dihedral : 7.020 57.706 3083 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -2.54 (0.16), residues: 2706 helix: -0.90 (0.23), residues: 425 sheet: -2.02 (0.17), residues: 806 loop : -1.69 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 36 HIS 0.008 0.002 HIS K 91 PHE 0.023 0.002 PHE A 145 TYR 0.027 0.002 TYR C 223 ARG 0.010 0.001 ARG K 54 *********************** 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 288 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.504 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: K 10 PHE cc_start: 0.7994 (t80) cc_final: 0.7603 (t80) REVERT: K 28 ASP cc_start: 0.7390 (t0) cc_final: 0.7184 (m-30) REVERT: K 50 TRP cc_start: 0.8539 (m100) cc_final: 0.8287 (m-90) REVERT: K 92 TYR cc_start: 0.7808 (t80) cc_final: 0.7607 (t80) REVERT: J 9 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8495 (mmtm) REVERT: G 12 MET cc_start: 0.8064 (mmp) cc_final: 0.7182 (mmm) REVERT: N 37 LEU cc_start: 0.8654 (mp) cc_final: 0.8222 (tt) REVERT: N 52 LEU cc_start: 0.9091 (mt) cc_final: 0.8577 (mt) REVERT: N 81 MET cc_start: 0.8826 (tmm) cc_final: 0.8614 (tmm) REVERT: N 114 LEU cc_start: 0.9314 (tp) cc_final: 0.8967 (tp) REVERT: L 11 LEU cc_start: 0.8460 (tp) cc_final: 0.8253 (tp) REVERT: L 19 LYS cc_start: 0.8597 (pptt) cc_final: 0.8214 (tmmt) REVERT: L 114 LEU cc_start: 0.9193 (mm) cc_final: 0.8452 (mm) REVERT: I 4 MET cc_start: 0.7999 (mmm) cc_final: 0.7341 (mmm) REVERT: I 11 MET cc_start: 0.7211 (mmm) cc_final: 0.6928 (mmm) REVERT: I 86 TYR cc_start: 0.8330 (m-10) cc_final: 0.7789 (m-10) REVERT: A 147 MET cc_start: 0.8503 (tpt) cc_final: 0.8175 (tpp) REVERT: A 246 MET cc_start: 0.4340 (ptt) cc_final: 0.3795 (ptm) REVERT: A 263 MET cc_start: 0.9047 (mmp) cc_final: 0.8676 (mmm) REVERT: A 287 MET cc_start: 0.8764 (tmm) cc_final: 0.8524 (tmm) REVERT: A 404 MET cc_start: 0.9265 (mmm) cc_final: 0.8976 (mmp) REVERT: E 147 MET cc_start: 0.8492 (ttp) cc_final: 0.8193 (ttt) REVERT: E 163 MET cc_start: 0.8471 (mmm) cc_final: 0.7982 (mmm) REVERT: E 287 MET cc_start: 0.9331 (ttm) cc_final: 0.8691 (tmm) REVERT: E 404 MET cc_start: 0.9270 (mmm) cc_final: 0.8970 (mmt) REVERT: E 411 MET cc_start: 0.9038 (ptp) cc_final: 0.8833 (ppp) REVERT: D 56 MET cc_start: 0.9169 (ttm) cc_final: 0.8264 (tpp) REVERT: D 140 MET cc_start: 0.7834 (mtm) cc_final: 0.6443 (mtm) REVERT: D 263 MET cc_start: 0.9226 (mmm) cc_final: 0.8308 (mmt) REVERT: D 404 MET cc_start: 0.9077 (mmm) cc_final: 0.8701 (mtt) REVERT: B 246 MET cc_start: 0.5464 (ptt) cc_final: 0.4819 (ppp) REVERT: B 404 MET cc_start: 0.8982 (mmm) cc_final: 0.8569 (mtt) REVERT: C 56 MET cc_start: 0.9286 (tpp) cc_final: 0.8761 (tpp) REVERT: C 246 MET cc_start: 0.6702 (ptt) cc_final: 0.6055 (ppp) REVERT: C 404 MET cc_start: 0.8768 (mmm) cc_final: 0.8281 (mtt) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3166 time to fit residues: 145.2233 Evaluate side-chains 234 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 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** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** E 186 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.9451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22428 Z= 0.344 Angle : 0.822 16.984 30398 Z= 0.412 Chirality : 0.047 0.225 3358 Planarity : 0.005 0.048 3808 Dihedral : 7.249 56.981 3083 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -2.59 (0.16), residues: 2706 helix: -0.78 (0.25), residues: 385 sheet: -2.14 (0.17), residues: 791 loop : -1.71 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 47 HIS 0.006 0.002 HIS C 201 PHE 0.028 0.002 PHE C 44 TYR 0.039 0.002 TYR J 87 ARG 0.008 0.001 ARG C 65 *********************** 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 284 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.737 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: K 10 PHE cc_start: 0.8053 (t80) cc_final: 0.7761 (t80) REVERT: K 28 ASP cc_start: 0.7554 (t0) cc_final: 0.7301 (m-30) REVERT: F 11 LEU cc_start: 0.8629 (tp) cc_final: 0.7923 (tp) REVERT: F 12 MET cc_start: 0.7377 (mmm) cc_final: 0.6790 (mmm) REVERT: J 9 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8549 (mmtm) REVERT: J 18 ARG cc_start: 0.9353 (ptm-80) cc_final: 0.8924 (ttp80) REVERT: G 12 MET cc_start: 0.7786 (mmp) cc_final: 0.7135 (mmm) REVERT: N 37 LEU cc_start: 0.8816 (mp) cc_final: 0.8338 (tt) REVERT: N 52 LEU cc_start: 0.9114 (mt) cc_final: 0.8608 (mt) REVERT: N 81 MET cc_start: 0.8858 (tmm) cc_final: 0.8631 (tmm) REVERT: M 10 PHE cc_start: 0.7624 (t80) cc_final: 0.7414 (t80) REVERT: M 11 MET cc_start: 0.5725 (mmt) cc_final: 0.5415 (mmp) REVERT: L 12 MET cc_start: 0.8243 (mmp) cc_final: 0.7707 (mmm) REVERT: L 19 LYS cc_start: 0.8583 (pptt) cc_final: 0.8079 (pptt) REVERT: I 4 MET cc_start: 0.8085 (mmm) cc_final: 0.7448 (mmm) REVERT: I 11 MET cc_start: 0.7379 (mmm) cc_final: 0.6966 (mmm) REVERT: I 86 TYR cc_start: 0.8408 (m-10) cc_final: 0.7725 (m-10) REVERT: A 147 MET cc_start: 0.8625 (tpt) cc_final: 0.8404 (tpp) REVERT: A 246 MET cc_start: 0.4482 (ptt) cc_final: 0.3934 (ptm) REVERT: A 263 MET cc_start: 0.9147 (mmp) cc_final: 0.8747 (mmm) REVERT: A 404 MET cc_start: 0.9276 (mmm) cc_final: 0.9027 (mmp) REVERT: E 147 MET cc_start: 0.8517 (ttp) cc_final: 0.8288 (ttt) REVERT: E 163 MET cc_start: 0.8466 (mmm) cc_final: 0.8016 (mmm) REVERT: E 287 MET cc_start: 0.9312 (ttm) cc_final: 0.9087 (ttm) REVERT: E 404 MET cc_start: 0.9325 (mmm) cc_final: 0.9036 (mmt) REVERT: D 56 MET cc_start: 0.9221 (ttm) cc_final: 0.8429 (tpp) REVERT: D 140 MET cc_start: 0.7827 (mtm) cc_final: 0.6682 (mtm) REVERT: D 147 MET cc_start: 0.8994 (pmm) cc_final: 0.8761 (pmm) REVERT: D 263 MET cc_start: 0.9303 (mmm) cc_final: 0.8387 (mmt) REVERT: D 404 MET cc_start: 0.9143 (mmm) cc_final: 0.8776 (mtt) REVERT: D 411 MET cc_start: 0.8368 (ptp) cc_final: 0.8164 (ppp) REVERT: B 246 MET cc_start: 0.5511 (ptt) cc_final: 0.5009 (ptp) REVERT: B 404 MET cc_start: 0.9023 (mmm) cc_final: 0.8665 (mtt) REVERT: C 56 MET cc_start: 0.9254 (tpp) cc_final: 0.8805 (tpp) REVERT: C 147 MET cc_start: 0.8951 (ttt) cc_final: 0.8683 (ttm) REVERT: C 220 MET cc_start: 0.7751 (mpp) cc_final: 0.7550 (mmm) REVERT: C 246 MET cc_start: 0.6782 (ptt) cc_final: 0.6107 (ppp) REVERT: C 404 MET cc_start: 0.8793 (mmm) cc_final: 0.8352 (mtt) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3508 time to fit residues: 157.6588 Evaluate side-chains 223 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 103 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 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** A 46 ASN 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.9539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22428 Z= 0.233 Angle : 0.744 14.894 30398 Z= 0.368 Chirality : 0.046 0.227 3358 Planarity : 0.004 0.042 3808 Dihedral : 6.837 56.439 3083 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.34 (0.16), residues: 2706 helix: -0.46 (0.25), residues: 385 sheet: -1.97 (0.17), residues: 783 loop : -1.59 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 47 HIS 0.005 0.001 HIS C 201 PHE 0.019 0.002 PHE E 409 TYR 0.025 0.002 TYR F 94 ARG 0.007 0.001 ARG K 54 *********************** 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 291 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.700 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: K 4 MET cc_start: 0.7493 (mpp) cc_final: 0.6234 (mpp) REVERT: K 28 ASP cc_start: 0.7428 (t0) cc_final: 0.7135 (m-30) REVERT: K 92 TYR cc_start: 0.7839 (t80) cc_final: 0.7609 (t80) REVERT: J 9 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8529 (mmtm) REVERT: J 18 ARG cc_start: 0.9320 (ptm-80) cc_final: 0.8896 (ttp80) REVERT: J 46 LEU cc_start: 0.8287 (tp) cc_final: 0.8071 (tp) REVERT: G 12 MET cc_start: 0.7712 (mmp) cc_final: 0.7114 (mmm) REVERT: O 50 TRP cc_start: 0.8994 (m100) cc_final: 0.8793 (m-90) REVERT: O 92 TYR cc_start: 0.8131 (t80) cc_final: 0.7916 (t80) REVERT: N 52 LEU cc_start: 0.9077 (mt) cc_final: 0.8577 (mt) REVERT: N 114 LEU cc_start: 0.9377 (tp) cc_final: 0.9113 (tp) REVERT: L 12 MET cc_start: 0.8014 (mmp) cc_final: 0.7554 (mmm) REVERT: L 19 LYS cc_start: 0.8421 (pptt) cc_final: 0.7872 (pptt) REVERT: L 81 MET cc_start: 0.8588 (tmm) cc_final: 0.8231 (ppp) REVERT: I 4 MET cc_start: 0.8018 (mmm) cc_final: 0.7400 (mmm) REVERT: I 11 MET cc_start: 0.7389 (mmm) cc_final: 0.7070 (mmm) REVERT: I 86 TYR cc_start: 0.8282 (m-10) cc_final: 0.7904 (m-10) REVERT: A 147 MET cc_start: 0.8676 (tpt) cc_final: 0.8297 (tpp) REVERT: A 246 MET cc_start: 0.4586 (ptt) cc_final: 0.3968 (ptm) REVERT: A 404 MET cc_start: 0.9273 (mmm) cc_final: 0.9021 (mmp) REVERT: E 157 GLU cc_start: 0.9054 (pt0) cc_final: 0.8828 (pt0) REVERT: E 163 MET cc_start: 0.8455 (mmm) cc_final: 0.8045 (mmm) REVERT: E 263 MET cc_start: 0.9332 (tpp) cc_final: 0.8840 (tpp) REVERT: E 287 MET cc_start: 0.9293 (ttm) cc_final: 0.8647 (tmm) REVERT: E 404 MET cc_start: 0.9285 (mmm) cc_final: 0.8987 (mmt) REVERT: D 56 MET cc_start: 0.9134 (ttm) cc_final: 0.8922 (tpp) REVERT: D 147 MET cc_start: 0.9023 (pmm) cc_final: 0.8744 (pmm) REVERT: D 263 MET cc_start: 0.9264 (mmm) cc_final: 0.8363 (mmt) REVERT: D 404 MET cc_start: 0.9139 (mmm) cc_final: 0.8769 (mmt) REVERT: B 220 MET cc_start: 0.8234 (mpp) cc_final: 0.7878 (mmm) REVERT: B 233 LEU cc_start: 0.9635 (tp) cc_final: 0.9414 (tp) REVERT: B 246 MET cc_start: 0.5577 (ptt) cc_final: 0.4746 (ppp) REVERT: B 404 MET cc_start: 0.9005 (mmm) cc_final: 0.8612 (mtt) REVERT: C 147 MET cc_start: 0.8945 (ttt) cc_final: 0.8565 (ttm) REVERT: C 246 MET cc_start: 0.6830 (ptt) cc_final: 0.6174 (ppp) REVERT: C 404 MET cc_start: 0.8753 (mmm) cc_final: 0.8290 (mtt) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3159 time to fit residues: 146.2687 Evaluate side-chains 234 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 72.5567 > 50: distance: 4 - 11: 28.636 distance: 11 - 12: 61.015 distance: 12 - 13: 28.503 distance: 12 - 15: 52.146 distance: 13 - 14: 55.419 distance: 13 - 19: 39.023 distance: 15 - 16: 67.461 distance: 16 - 17: 35.032 distance: 19 - 20: 47.996 distance: 20 - 21: 25.550 distance: 20 - 23: 44.288 distance: 21 - 22: 39.418 distance: 21 - 27: 38.360 distance: 23 - 24: 23.281 distance: 24 - 25: 67.200 distance: 25 - 26: 41.967 distance: 28 - 29: 44.053 distance: 28 - 31: 40.859 distance: 29 - 30: 40.972 distance: 29 - 36: 44.195 distance: 31 - 32: 52.118 distance: 32 - 33: 65.429 distance: 33 - 34: 46.099 distance: 34 - 35: 45.401 distance: 36 - 37: 47.495 distance: 36 - 42: 62.148 distance: 37 - 38: 48.131 distance: 37 - 40: 14.901 distance: 38 - 39: 38.943 distance: 38 - 43: 40.703 distance: 40 - 41: 27.199 distance: 41 - 42: 49.870 distance: 43 - 44: 64.058 distance: 44 - 45: 30.063 distance: 45 - 46: 39.127 distance: 45 - 47: 55.306 distance: 47 - 48: 39.883 distance: 48 - 49: 33.745 distance: 48 - 51: 36.894 distance: 49 - 50: 27.959 distance: 49 - 52: 36.243 distance: 53 - 54: 27.772 distance: 53 - 56: 69.140 distance: 54 - 55: 9.985 distance: 54 - 57: 48.272 distance: 57 - 58: 39.541 distance: 58 - 59: 57.643 distance: 58 - 61: 39.994 distance: 59 - 60: 56.522 distance: 59 - 64: 40.582 distance: 64 - 65: 11.308 distance: 65 - 66: 39.429 distance: 65 - 68: 11.705 distance: 66 - 73: 54.540 distance: 68 - 69: 8.329 distance: 69 - 70: 18.345 distance: 70 - 71: 50.433 distance: 71 - 72: 31.249 distance: 73 - 74: 13.075 distance: 73 - 105: 23.898 distance: 74 - 75: 39.315 distance: 74 - 77: 3.876 distance: 75 - 81: 34.402 distance: 76 - 102: 33.713 distance: 77 - 78: 40.972 distance: 77 - 79: 38.603 distance: 78 - 80: 39.762