Starting phenix.real_space_refine on Sat Nov 18 06:00:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/11_2023/7mlu_23910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/11_2023/7mlu_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_23910/11_2023/7mlu_23910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/11_2023/7mlu_23910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/11_2023/7mlu_23910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlu_23910/11_2023/7mlu_23910.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21886 Number of models: 1 Model: "" Number of chains: 20 Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "O" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.25, per 1000 atoms: 0.51 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: 8.00 Conformation dependent library (CDL) restraints added in 3.8 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: 2.47 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: 7.00 Time building geometry restraints manager: 8.64 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: 12504 14.39 - 28.78: 563 28.78 - 43.17: 128 43.17 - 57.56: 17 57.56 - 71.95: 17 Dihedral angle restraints: 13229 sinusoidal: 5254 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 13226 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 2.440 nonbonded pdb=" OG1 THR E 162 " pdb=" OD1 ASN E 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR C 162 " pdb=" OD1 ASN C 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR A 162 " pdb=" OD1 ASN A 164 " model vdw 2.271 2.440 ... (remaining 172776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'I' and resid 2 through 102) selection = chain 'J' selection = (chain 'K' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) selection = (chain 'M' and resid 2 through 102) selection = (chain 'O' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 14.250 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 55.200 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.150 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.130 ------------------------------------------------------------------------------- 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 : 9.475 71.951 8057 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 *********************** 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 : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 595 average time/residue: 0.3775 time to fit residues: 333.2182 Evaluate side-chains 323 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 5.9990 chunk 204 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 HIS K 37 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 115 ASN A 125 ASN A 164 ASN A 177 GLN A 186 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN E 61 ASN E 67 GLN E 115 ASN E 125 ASN E 186 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN D 61 ASN D 67 GLN D 125 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 305 ASN B 61 ASN B 67 GLN B 125 ASN B 177 GLN B 186 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 61 ASN C 67 GLN C 115 ASN C 125 ASN C 177 GLN C 186 GLN C 226 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22428 Z= 0.165 Angle : 0.664 14.397 30398 Z= 0.331 Chirality : 0.044 0.283 3358 Planarity : 0.005 0.054 3808 Dihedral : 5.547 27.387 2978 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % 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: -3.19 (0.14), residues: 2706 helix: -2.33 (0.20), residues: 455 sheet: -1.75 (0.17), residues: 733 loop : -2.25 (0.15), residues: 1518 *********************** 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 436 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 436 average time/residue: 0.3525 time to fit residues: 235.6947 Evaluate side-chains 305 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3503 ------------------------------------------------------------------------------- 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: 20.0000 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.4980 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN N 43 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN I 38 GLN A 226 GLN A 305 ASN ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN C 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22428 Z= 0.280 Angle : 0.761 14.690 30398 Z= 0.384 Chirality : 0.045 0.274 3358 Planarity : 0.005 0.052 3808 Dihedral : 5.780 25.197 2978 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 0.04 % Allowed : 2.31 % 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: -2.61 (0.15), residues: 2706 helix: -1.14 (0.23), residues: 460 sheet: -1.71 (0.18), residues: 734 loop : -1.93 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.371 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 outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.3513 time to fit residues: 196.9259 Evaluate side-chains 266 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3008 ------------------------------------------------------------------------------- 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: 5.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 246 optimal weight: 0.9980 chunk 260 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS M 89 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 305 ASN E 67 GLN E 107 HIS ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 226 GLN C 46 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 22428 Z= 0.321 Angle : 0.790 15.548 30398 Z= 0.396 Chirality : 0.046 0.332 3358 Planarity : 0.005 0.078 3808 Dihedral : 6.109 24.878 2978 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 30.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2706 helix: -0.92 (0.23), residues: 460 sheet: -1.77 (0.18), residues: 793 loop : -1.77 (0.17), residues: 1453 *********************** 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 314 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 312 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 313 average time/residue: 0.3675 time to fit residues: 177.2204 Evaluate side-chains 242 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2639 time to fit residues: 3.9561 ------------------------------------------------------------------------------- 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: 2.9990 chunk 148 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN A 67 GLN 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 177 GLN B 46 ASN C 46 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22428 Z= 0.211 Angle : 0.682 15.918 30398 Z= 0.337 Chirality : 0.044 0.252 3358 Planarity : 0.004 0.047 3808 Dihedral : 5.679 25.537 2978 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.04 % Allowed : 2.27 % Favored : 97.69 % 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: -2.10 (0.16), residues: 2706 helix: -0.55 (0.25), residues: 420 sheet: -1.56 (0.18), residues: 771 loop : -1.52 (0.17), residues: 1515 *********************** 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 320 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 2.697 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 outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.3608 time to fit residues: 180.6756 Evaluate side-chains 250 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3183 ------------------------------------------------------------------------------- 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: 1.9990 chunk 235 optimal weight: 0.0030 chunk 51 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 137 optimal weight: 6.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 HIS A 67 GLN E 46 ASN E 305 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN C 46 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 22428 Z= 0.299 Angle : 0.764 15.459 30398 Z= 0.381 Chirality : 0.045 0.243 3358 Planarity : 0.005 0.086 3808 Dihedral : 5.984 24.686 2978 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 30.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.22 (0.16), residues: 2706 helix: -0.53 (0.24), residues: 420 sheet: -1.82 (0.18), residues: 794 loop : -1.51 (0.17), residues: 1492 *********************** 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 300 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.733 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 outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3414 time to fit residues: 161.1847 Evaluate side-chains 230 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4693 ------------------------------------------------------------------------------- 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: 20.0000 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 67 GLN 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** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22428 Z= 0.294 Angle : 0.761 16.117 30398 Z= 0.377 Chirality : 0.045 0.242 3358 Planarity : 0.005 0.047 3808 Dihedral : 6.057 24.006 2978 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 31.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -2.24 (0.16), residues: 2706 helix: -0.46 (0.24), residues: 420 sheet: -1.62 (0.19), residues: 704 loop : -1.72 (0.16), residues: 1582 *********************** 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 293 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.476 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 outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.3524 time to fit residues: 160.1091 Evaluate side-chains 234 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 128 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN M 89 GLN A 46 ASN A 305 ASN ** E 177 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22428 Z= 0.166 Angle : 0.677 14.356 30398 Z= 0.329 Chirality : 0.045 0.253 3358 Planarity : 0.004 0.040 3808 Dihedral : 5.529 23.861 2978 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.04 % Allowed : 1.01 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2706 helix: -0.08 (0.26), residues: 410 sheet: -1.41 (0.18), residues: 724 loop : -1.50 (0.16), residues: 1572 *********************** 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 317 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 2.622 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 outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.3358 time to fit residues: 166.7931 Evaluate side-chains 251 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 219 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN A 46 ASN A 67 GLN ** E 177 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.9234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22428 Z= 0.273 Angle : 0.755 18.654 30398 Z= 0.372 Chirality : 0.045 0.248 3358 Planarity : 0.005 0.064 3808 Dihedral : 5.837 23.029 2978 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 30.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % 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: -2.01 (0.16), residues: 2706 helix: -0.06 (0.26), residues: 380 sheet: -1.57 (0.18), residues: 719 loop : -1.55 (0.16), residues: 1607 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.569 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 outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3427 time to fit residues: 153.3405 Evaluate side-chains 233 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 156 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 67 GLN ** E 177 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.9351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22428 Z= 0.188 Angle : 0.698 13.978 30398 Z= 0.340 Chirality : 0.045 0.252 3358 Planarity : 0.004 0.039 3808 Dihedral : 5.588 22.722 2978 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2706 helix: 0.20 (0.27), residues: 380 sheet: -1.39 (0.19), residues: 709 loop : -1.50 (0.16), residues: 1617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.584 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 outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3333 time to fit residues: 156.4172 Evaluate side-chains 244 residues out of total 2386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.3980 chunk 228 optimal weight: 7.9990 chunk 65 optimal weight: 0.0970 chunk 197 optimal weight: 8.9990 chunk 31 optimal weight: 0.0050 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.0010 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.041272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.033825 restraints weight = 247987.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.034603 restraints weight = 177757.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.035176 restraints weight = 137571.270| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.9436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22428 Z= 0.155 Angle : 0.675 12.019 30398 Z= 0.328 Chirality : 0.045 0.263 3358 Planarity : 0.004 0.057 3808 Dihedral : 5.244 22.894 2978 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2706 helix: 0.47 (0.28), residues: 380 sheet: -1.43 (0.19), residues: 706 loop : -1.30 (0.16), residues: 1620 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4432.05 seconds wall clock time: 82 minutes 33.29 seconds (4953.29 seconds total)