Starting phenix.real_space_refine on Tue Mar 19 03:03:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/03_2024/6pbx_20294.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 128 5.16 5 C 14880 2.51 5 N 3836 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E ASP 494": "OD1" <-> "OD2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ASP 560": "OD1" <-> "OD2" Residue "E ARG 564": "NH1" <-> "NH2" Residue "E PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 604": "OD1" <-> "OD2" Residue "E ARG 666": "NH1" <-> "NH2" Residue "E ARG 675": "NH1" <-> "NH2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ASP 264": "OD1" <-> "OD2" Residue "G TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 493": "NH1" <-> "NH2" Residue "G ASP 494": "OD1" <-> "OD2" Residue "G ARG 508": "NH1" <-> "NH2" Residue "G ASP 560": "OD1" <-> "OD2" Residue "G ARG 564": "NH1" <-> "NH2" Residue "G PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 604": "OD1" <-> "OD2" Residue "G ARG 666": "NH1" <-> "NH2" Residue "G ARG 675": "NH1" <-> "NH2" Residue "G GLU 692": "OE1" <-> "OE2" Residue "G PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23028 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 225 Chain: "E" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 225 Chain: "G" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 225 Chain: "D" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "H" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Time building chain proxies: 11.41, per 1000 atoms: 0.50 Number of scatterers: 23028 At special positions: 0 Unit cell: (157, 157, 142, 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 128 16.00 O 4184 8.00 N 3836 7.00 C 14880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 4.2 seconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 16 sheets defined 64.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 215 through 241 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS A 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.848A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 215 through 241 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.635A pdb=" N LYS C 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.693A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 520 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 removed outlier: 3.829A pdb=" N GLU C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.806A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 215 through 241 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS E 327 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 520 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU E 624 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 692 Processing helix chain 'E' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.804A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 Processing helix chain 'G' and resid 215 through 241 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 285 through 295 Processing helix chain 'G' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 379 removed outlier: 3.807A pdb=" N LEU G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 520 Processing helix chain 'G' and resid 524 through 532 Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU G 624 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'G' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.598A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 125 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.236A pdb=" N ASP E 641 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 618 " --> pdb=" O TYR E 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA E 628 " --> pdb=" O VAL E 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 125 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP G 641 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 618 " --> pdb=" O TYR G 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA G 628 " --> pdb=" O VAL G 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4236 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: 7.96 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7379 1.34 - 1.46: 5112 1.46 - 1.58: 10837 1.58 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 23524 Sorted by residual: bond pdb=" C LEU C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.52e+00 bond pdb=" C LEU A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.43e+00 bond pdb=" CG1 ILE C 224 " pdb=" CD1 ILE C 224 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" C LEU G 195 " pdb=" N PRO G 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.39e+00 bond pdb=" CG1 ILE A 224 " pdb=" CD1 ILE A 224 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.33e+00 ... (remaining 23519 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.33: 443 106.33 - 113.32: 12933 113.32 - 120.30: 9206 120.30 - 127.29: 9266 127.29 - 134.28: 252 Bond angle restraints: 32100 Sorted by residual: angle pdb=" N LEU C 195 " pdb=" CA LEU C 195 " pdb=" C LEU C 195 " ideal model delta sigma weight residual 109.81 119.83 -10.02 2.21e+00 2.05e-01 2.06e+01 angle pdb=" N LEU A 195 " pdb=" CA LEU A 195 " pdb=" C LEU A 195 " ideal model delta sigma weight residual 109.81 119.81 -10.00 2.21e+00 2.05e-01 2.05e+01 angle pdb=" N LEU E 195 " pdb=" CA LEU E 195 " pdb=" C LEU E 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" N LEU G 195 " pdb=" CA LEU G 195 " pdb=" C LEU G 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" CA PRO G 196 " pdb=" N PRO G 196 " pdb=" CD PRO G 196 " ideal model delta sigma weight residual 112.00 106.68 5.32 1.40e+00 5.10e-01 1.44e+01 ... (remaining 32095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 12216 16.35 - 32.69: 1068 32.69 - 49.04: 284 49.04 - 65.39: 44 65.39 - 81.74: 8 Dihedral angle restraints: 13620 sinusoidal: 4404 harmonic: 9216 Sorted by residual: dihedral pdb=" CA PRO G 502 " pdb=" C PRO G 502 " pdb=" N LYS G 503 " pdb=" CA LYS G 503 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO E 502 " pdb=" C PRO E 502 " pdb=" N LYS E 503 " pdb=" CA LYS E 503 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO A 502 " pdb=" C PRO A 502 " pdb=" N LYS A 503 " pdb=" CA LYS A 503 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2618 0.045 - 0.090: 851 0.090 - 0.134: 253 0.134 - 0.179: 50 0.179 - 0.224: 16 Chirality restraints: 3788 Sorted by residual: chirality pdb=" CB THR E 228 " pdb=" CA THR E 228 " pdb=" OG1 THR E 228 " pdb=" CG2 THR E 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR G 228 " pdb=" CA THR G 228 " pdb=" OG1 THR G 228 " pdb=" CG2 THR G 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 432 " pdb=" CA THR A 432 " pdb=" OG1 THR A 432 " pdb=" CG2 THR A 432 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3785 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 169 " -0.047 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 170 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO G 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 170 " -0.039 5.00e-02 4.00e+02 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6400 2.79 - 3.32: 22457 3.32 - 3.85: 40104 3.85 - 4.37: 43824 4.37 - 4.90: 73821 Nonbonded interactions: 186606 Sorted by model distance: nonbonded pdb=" O VAL E 172 " pdb=" OG SER F 38 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR C 582 " pdb=" OG SER C 590 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR A 582 " pdb=" OG SER A 590 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR G 582 " pdb=" OG SER G 590 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR E 582 " pdb=" OG SER E 590 " model vdw 2.281 2.440 ... (remaining 186601 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.010 Extract box with map and model: 8.460 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 60.180 Find NCS groups from input model: 1.320 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: 0.000 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: 76.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 23524 Z= 0.394 Angle : 0.825 11.343 32100 Z= 0.454 Chirality : 0.050 0.224 3788 Planarity : 0.006 0.069 4076 Dihedral : 14.043 81.736 7636 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.12), residues: 3088 helix: -2.01 (0.09), residues: 1760 sheet: -2.23 (0.33), residues: 204 loop : -1.70 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 370 HIS 0.010 0.002 HIS G 543 PHE 0.017 0.002 PHE F 68 TYR 0.017 0.002 TYR C 44 ARG 0.016 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.381 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: A 59 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9046 (mp0) REVERT: A 102 LYS cc_start: 0.9131 (tttp) cc_final: 0.8925 (ttmt) REVERT: A 468 PHE cc_start: 0.8574 (m-80) cc_final: 0.8372 (m-10) REVERT: A 470 ASN cc_start: 0.9215 (t0) cc_final: 0.9013 (t0) REVERT: A 519 MET cc_start: 0.8441 (ttm) cc_final: 0.7910 (tmm) REVERT: B 32 LEU cc_start: 0.8035 (tp) cc_final: 0.7779 (mt) REVERT: B 123 GLU cc_start: 0.8476 (tp30) cc_final: 0.8270 (tp30) REVERT: B 144 MET cc_start: 0.8239 (tpt) cc_final: 0.7685 (tpt) REVERT: C 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9022 (mp0) REVERT: C 99 MET cc_start: 0.8998 (mtp) cc_final: 0.8383 (mtp) REVERT: C 468 PHE cc_start: 0.8455 (m-80) cc_final: 0.8192 (m-10) REVERT: C 470 ASN cc_start: 0.9197 (t0) cc_final: 0.8987 (t0) REVERT: C 519 MET cc_start: 0.8459 (ttm) cc_final: 0.7996 (tmm) REVERT: C 651 GLN cc_start: 0.8796 (mt0) cc_final: 0.8553 (mt0) REVERT: C 652 LYS cc_start: 0.8829 (mttt) cc_final: 0.8618 (mmtm) REVERT: E 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9011 (mp0) REVERT: E 99 MET cc_start: 0.8988 (mtp) cc_final: 0.8360 (mtp) REVERT: E 470 ASN cc_start: 0.9164 (t0) cc_final: 0.8935 (t0) REVERT: E 519 MET cc_start: 0.8470 (ttm) cc_final: 0.8031 (tmm) REVERT: E 651 GLN cc_start: 0.8823 (mt0) cc_final: 0.8579 (mt0) REVERT: E 652 LYS cc_start: 0.8827 (mttt) cc_final: 0.8617 (mmtm) REVERT: G 60 VAL cc_start: 0.9278 (t) cc_final: 0.9073 (p) REVERT: G 463 LEU cc_start: 0.9183 (mt) cc_final: 0.8960 (mt) REVERT: G 468 PHE cc_start: 0.8441 (m-80) cc_final: 0.7997 (m-80) REVERT: G 470 ASN cc_start: 0.9256 (t0) cc_final: 0.8894 (t0) REVERT: G 519 MET cc_start: 0.8443 (ttm) cc_final: 0.7842 (tmm) REVERT: D 32 LEU cc_start: 0.8061 (tp) cc_final: 0.7540 (mt) REVERT: D 123 GLU cc_start: 0.8517 (tp30) cc_final: 0.8311 (tp30) REVERT: D 144 MET cc_start: 0.8203 (tpt) cc_final: 0.7661 (tpt) REVERT: F 32 LEU cc_start: 0.8253 (tp) cc_final: 0.8027 (mt) REVERT: F 119 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 123 GLU cc_start: 0.8518 (tp30) cc_final: 0.8313 (mm-30) REVERT: F 139 GLU cc_start: 0.9275 (mp0) cc_final: 0.8798 (pm20) REVERT: F 144 MET cc_start: 0.8165 (tpt) cc_final: 0.7622 (tpt) REVERT: H 139 GLU cc_start: 0.9250 (mp0) cc_final: 0.8787 (pm20) REVERT: H 144 MET cc_start: 0.8137 (tpt) cc_final: 0.7568 (tpt) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.3105 time to fit residues: 236.2746 Evaluate side-chains 329 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 486 HIS A 545 ASN A 651 GLN A 673 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN C 486 HIS C 673 ASN E 89 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN E 486 HIS E 673 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 GLN G 486 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23524 Z= 0.224 Angle : 0.574 8.239 32100 Z= 0.304 Chirality : 0.039 0.173 3788 Planarity : 0.004 0.047 4076 Dihedral : 4.592 16.357 3328 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.08 % Allowed : 13.79 % Favored : 85.13 % 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: -0.91 (0.14), residues: 3088 helix: -0.11 (0.11), residues: 1852 sheet: -1.45 (0.35), residues: 204 loop : -1.10 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 517 HIS 0.005 0.001 HIS G 543 PHE 0.023 0.001 PHE E 468 TYR 0.017 0.002 TYR A 512 ARG 0.006 0.001 ARG C 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 363 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.7445 (m-30) cc_final: 0.7227 (t0) REVERT: A 373 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8527 (tt) REVERT: A 478 MET cc_start: 0.8390 (mtp) cc_final: 0.8047 (ttm) REVERT: A 519 MET cc_start: 0.8459 (ttm) cc_final: 0.7888 (tmm) REVERT: A 536 MET cc_start: 0.8517 (mmm) cc_final: 0.8214 (mtp) REVERT: B 139 GLU cc_start: 0.9253 (mp0) cc_final: 0.8810 (pm20) REVERT: B 144 MET cc_start: 0.8036 (tpt) cc_final: 0.7586 (tpt) REVERT: C 59 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8975 (mp0) REVERT: C 258 ASP cc_start: 0.7493 (m-30) cc_final: 0.7260 (t0) REVERT: C 373 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8526 (tt) REVERT: C 478 MET cc_start: 0.8335 (mtp) cc_final: 0.8009 (ttm) REVERT: C 519 MET cc_start: 0.8443 (ttm) cc_final: 0.7857 (tmm) REVERT: E 258 ASP cc_start: 0.7488 (m-30) cc_final: 0.7269 (t0) REVERT: E 373 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8525 (tt) REVERT: E 478 MET cc_start: 0.8331 (mtp) cc_final: 0.7999 (ttm) REVERT: E 519 MET cc_start: 0.8464 (ttm) cc_final: 0.7893 (tmm) REVERT: G 258 ASP cc_start: 0.7507 (m-30) cc_final: 0.7215 (t0) REVERT: G 468 PHE cc_start: 0.8311 (m-80) cc_final: 0.7873 (m-80) REVERT: D 32 LEU cc_start: 0.7701 (tp) cc_final: 0.7498 (mt) REVERT: D 144 MET cc_start: 0.8126 (tpt) cc_final: 0.7739 (tpt) REVERT: F 139 GLU cc_start: 0.9258 (mp0) cc_final: 0.8797 (pm20) REVERT: F 144 MET cc_start: 0.8106 (tpt) cc_final: 0.7610 (tpt) REVERT: H 139 GLU cc_start: 0.9220 (mp0) cc_final: 0.8729 (pm20) REVERT: H 144 MET cc_start: 0.8024 (tpt) cc_final: 0.7525 (tpt) outliers start: 23 outliers final: 5 residues processed: 375 average time/residue: 0.2809 time to fit residues: 174.3327 Evaluate side-chains 311 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 303 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 426 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 50.0000 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 306 optimal weight: 0.1980 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN C 89 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN E 651 GLN G 89 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN G 651 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23524 Z= 0.183 Angle : 0.534 8.748 32100 Z= 0.277 Chirality : 0.038 0.137 3788 Planarity : 0.003 0.039 4076 Dihedral : 4.190 15.881 3328 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 15.99 % Favored : 82.41 % 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: 0.17 (0.15), residues: 3088 helix: 0.83 (0.12), residues: 1872 sheet: -0.89 (0.37), residues: 200 loop : -0.89 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 517 HIS 0.004 0.001 HIS G 543 PHE 0.024 0.001 PHE E 17 TYR 0.015 0.001 TYR A 512 ARG 0.004 0.000 ARG G 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 341 time to evaluate : 2.823 Fit side-chains REVERT: A 373 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 377 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8871 (mm-30) REVERT: A 431 MET cc_start: 0.9038 (mmm) cc_final: 0.8806 (tpp) REVERT: A 478 MET cc_start: 0.8330 (mtp) cc_final: 0.8075 (ttm) REVERT: A 519 MET cc_start: 0.8462 (ttm) cc_final: 0.7882 (tmm) REVERT: B 139 GLU cc_start: 0.9262 (mp0) cc_final: 0.8822 (pm20) REVERT: B 144 MET cc_start: 0.7962 (tpt) cc_final: 0.7511 (tpt) REVERT: C 373 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8454 (tt) REVERT: C 377 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8861 (mm-30) REVERT: C 478 MET cc_start: 0.8313 (mtp) cc_final: 0.8063 (ttm) REVERT: C 519 MET cc_start: 0.8488 (ttm) cc_final: 0.7929 (tmm) REVERT: E 373 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8451 (tt) REVERT: E 377 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8859 (mm-30) REVERT: E 478 MET cc_start: 0.8322 (mtp) cc_final: 0.8063 (ttm) REVERT: E 519 MET cc_start: 0.8506 (ttm) cc_final: 0.7952 (tmm) REVERT: E 536 MET cc_start: 0.8425 (mmm) cc_final: 0.8171 (mtp) REVERT: G 258 ASP cc_start: 0.7560 (m-30) cc_final: 0.7295 (t0) REVERT: G 364 HIS cc_start: 0.8486 (t70) cc_final: 0.8089 (t-170) REVERT: G 375 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: G 464 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7733 (t80) REVERT: G 468 PHE cc_start: 0.8039 (m-80) cc_final: 0.7597 (m-80) REVERT: G 536 MET cc_start: 0.8541 (mmm) cc_final: 0.8140 (mtp) REVERT: D 144 MET cc_start: 0.8008 (tpt) cc_final: 0.7547 (tpt) REVERT: F 144 MET cc_start: 0.8017 (tpt) cc_final: 0.7570 (tpt) REVERT: H 139 GLU cc_start: 0.9261 (mp0) cc_final: 0.8734 (pm20) REVERT: H 144 MET cc_start: 0.8024 (tpt) cc_final: 0.7514 (tpt) outliers start: 34 outliers final: 12 residues processed: 364 average time/residue: 0.2854 time to fit residues: 171.8584 Evaluate side-chains 318 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 301 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 0.0870 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23524 Z= 0.192 Angle : 0.543 10.256 32100 Z= 0.277 Chirality : 0.038 0.138 3788 Planarity : 0.003 0.038 4076 Dihedral : 3.982 15.534 3328 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.02 % Allowed : 18.53 % Favored : 79.46 % 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: 0.77 (0.16), residues: 3088 helix: 1.33 (0.13), residues: 1864 sheet: -0.67 (0.37), residues: 200 loop : -0.68 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 391 HIS 0.004 0.001 HIS G 543 PHE 0.027 0.001 PHE G 17 TYR 0.014 0.001 TYR E 512 ARG 0.005 0.000 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 2.731 Fit side-chains REVERT: A 373 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 375 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8732 (m-30) REVERT: A 431 MET cc_start: 0.9045 (mmm) cc_final: 0.8830 (tpp) REVERT: A 457 MET cc_start: 0.8579 (mtm) cc_final: 0.8310 (mtp) REVERT: A 478 MET cc_start: 0.8304 (mtp) cc_final: 0.8079 (ttm) REVERT: A 519 MET cc_start: 0.8458 (ttm) cc_final: 0.7867 (tmm) REVERT: A 536 MET cc_start: 0.8531 (mmm) cc_final: 0.8138 (mtp) REVERT: B 139 GLU cc_start: 0.9243 (mp0) cc_final: 0.8749 (pm20) REVERT: B 144 MET cc_start: 0.7974 (tpt) cc_final: 0.7512 (tpt) REVERT: C 373 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8469 (tt) REVERT: C 375 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8715 (m-30) REVERT: C 457 MET cc_start: 0.8522 (mtm) cc_final: 0.8311 (mtp) REVERT: C 478 MET cc_start: 0.8282 (mtp) cc_final: 0.8073 (ttm) REVERT: E 373 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8479 (tt) REVERT: E 375 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8711 (m-30) REVERT: E 377 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8967 (mm-30) REVERT: E 457 MET cc_start: 0.8586 (mtm) cc_final: 0.8317 (mtp) REVERT: E 478 MET cc_start: 0.8331 (mtp) cc_final: 0.8105 (ttm) REVERT: E 519 MET cc_start: 0.8506 (ttm) cc_final: 0.7925 (tmm) REVERT: G 258 ASP cc_start: 0.7574 (m-30) cc_final: 0.7367 (t0) REVERT: G 375 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: G 377 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8931 (mm-30) REVERT: D 144 MET cc_start: 0.8025 (tpt) cc_final: 0.7569 (tpt) REVERT: F 144 MET cc_start: 0.8061 (tpt) cc_final: 0.7568 (tpt) REVERT: H 139 GLU cc_start: 0.9224 (mp0) cc_final: 0.8705 (pm20) REVERT: H 144 MET cc_start: 0.8050 (tpt) cc_final: 0.7552 (tpt) outliers start: 43 outliers final: 22 residues processed: 361 average time/residue: 0.2931 time to fit residues: 175.5821 Evaluate side-chains 332 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 303 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 644 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 ASN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23524 Z= 0.395 Angle : 0.678 12.559 32100 Z= 0.351 Chirality : 0.042 0.183 3788 Planarity : 0.004 0.043 4076 Dihedral : 4.379 17.572 3328 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.63 % Allowed : 21.53 % Favored : 75.84 % 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: 0.51 (0.16), residues: 3088 helix: 1.10 (0.12), residues: 1864 sheet: -0.93 (0.37), residues: 204 loop : -0.70 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 517 HIS 0.009 0.002 HIS A 543 PHE 0.022 0.002 PHE E 17 TYR 0.019 0.002 TYR G 237 ARG 0.005 0.001 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 313 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8726 (m-30) REVERT: B 139 GLU cc_start: 0.9289 (mp0) cc_final: 0.8890 (pm20) REVERT: B 144 MET cc_start: 0.8022 (tpt) cc_final: 0.7524 (tpt) REVERT: C 375 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8838 (m-30) REVERT: E 373 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8457 (tt) REVERT: E 375 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8853 (m-30) REVERT: E 377 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8968 (mm-30) REVERT: E 457 MET cc_start: 0.8786 (mtm) cc_final: 0.8192 (mtp) REVERT: G 375 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8825 (m-30) REVERT: D 144 MET cc_start: 0.8062 (tpt) cc_final: 0.7584 (tpt) REVERT: F 139 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8531 (pm20) REVERT: F 144 MET cc_start: 0.8090 (tpt) cc_final: 0.7580 (tpt) REVERT: H 139 GLU cc_start: 0.9244 (mp0) cc_final: 0.8779 (pm20) REVERT: H 144 MET cc_start: 0.8088 (tpt) cc_final: 0.7578 (tpt) outliers start: 56 outliers final: 34 residues processed: 350 average time/residue: 0.2904 time to fit residues: 167.3871 Evaluate side-chains 333 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 294 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain F residue 141 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 0.0670 chunk 74 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23524 Z= 0.154 Angle : 0.539 10.646 32100 Z= 0.273 Chirality : 0.039 0.157 3788 Planarity : 0.003 0.040 4076 Dihedral : 3.896 15.759 3328 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.78 % Allowed : 22.51 % Favored : 75.70 % 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: 1.10 (0.16), residues: 3088 helix: 1.58 (0.13), residues: 1864 sheet: -0.65 (0.37), residues: 200 loop : -0.48 (0.22), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 391 HIS 0.003 0.001 HIS C 543 PHE 0.027 0.001 PHE A 17 TYR 0.020 0.001 TYR A 464 ARG 0.003 0.000 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 343 time to evaluate : 2.590 Fit side-chains REVERT: B 126 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7559 (mtp180) REVERT: B 139 GLU cc_start: 0.9303 (mp0) cc_final: 0.8893 (pm20) REVERT: B 144 MET cc_start: 0.8063 (tpt) cc_final: 0.7607 (tpt) REVERT: C 375 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8823 (m-30) REVERT: E 375 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8898 (m-30) REVERT: E 377 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8975 (mm-30) REVERT: E 457 MET cc_start: 0.8553 (mtm) cc_final: 0.8309 (mtp) REVERT: G 364 HIS cc_start: 0.8401 (t70) cc_final: 0.8074 (t-170) REVERT: G 536 MET cc_start: 0.8582 (mmm) cc_final: 0.8155 (mtp) REVERT: G 568 MET cc_start: 0.8723 (mtt) cc_final: 0.8404 (mmm) REVERT: D 144 MET cc_start: 0.8065 (tpt) cc_final: 0.7621 (tpt) REVERT: F 144 MET cc_start: 0.8055 (tpt) cc_final: 0.7568 (tpt) REVERT: H 139 GLU cc_start: 0.9202 (mp0) cc_final: 0.8738 (pm20) REVERT: H 144 MET cc_start: 0.8038 (tpt) cc_final: 0.7811 (ptt) outliers start: 38 outliers final: 25 residues processed: 373 average time/residue: 0.2965 time to fit residues: 181.9989 Evaluate side-chains 334 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 307 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23524 Z= 0.175 Angle : 0.566 12.470 32100 Z= 0.286 Chirality : 0.039 0.191 3788 Planarity : 0.003 0.040 4076 Dihedral : 3.825 15.369 3328 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.78 % Allowed : 24.20 % Favored : 74.02 % 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: 1.21 (0.16), residues: 3088 helix: 1.70 (0.13), residues: 1860 sheet: -0.59 (0.37), residues: 200 loop : -0.50 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 365 HIS 0.005 0.001 HIS A 364 PHE 0.030 0.001 PHE A 17 TYR 0.016 0.001 TYR A 464 ARG 0.009 0.000 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 321 time to evaluate : 2.688 Fit side-chains REVERT: A 375 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8786 (m-30) REVERT: B 139 GLU cc_start: 0.9291 (mp0) cc_final: 0.8891 (pm20) REVERT: B 144 MET cc_start: 0.8028 (tpt) cc_final: 0.7575 (tpt) REVERT: C 375 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: E 375 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8881 (m-30) REVERT: E 377 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8983 (mm-30) REVERT: G 364 HIS cc_start: 0.8486 (t70) cc_final: 0.8240 (t-170) REVERT: G 431 MET cc_start: 0.8994 (tpp) cc_final: 0.8696 (tpp) REVERT: G 539 ASP cc_start: 0.9382 (t0) cc_final: 0.9119 (m-30) REVERT: G 568 MET cc_start: 0.8729 (mtt) cc_final: 0.8452 (mmm) REVERT: D 139 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8453 (pm20) REVERT: D 144 MET cc_start: 0.8083 (tpt) cc_final: 0.7732 (tpp) REVERT: F 144 MET cc_start: 0.8079 (tpt) cc_final: 0.7607 (tpt) REVERT: H 139 GLU cc_start: 0.9197 (mp0) cc_final: 0.8740 (pm20) REVERT: H 144 MET cc_start: 0.8027 (tpt) cc_final: 0.7549 (tpt) outliers start: 38 outliers final: 25 residues processed: 355 average time/residue: 0.2916 time to fit residues: 171.8364 Evaluate side-chains 334 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 306 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23524 Z= 0.184 Angle : 0.567 11.908 32100 Z= 0.288 Chirality : 0.039 0.186 3788 Planarity : 0.003 0.034 4076 Dihedral : 3.807 15.947 3328 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.83 % Allowed : 24.30 % Favored : 73.87 % 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: 1.28 (0.16), residues: 3088 helix: 1.76 (0.13), residues: 1864 sheet: -0.63 (0.37), residues: 200 loop : -0.49 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 517 HIS 0.006 0.001 HIS E 364 PHE 0.030 0.001 PHE C 17 TYR 0.012 0.001 TYR E 512 ARG 0.006 0.000 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 318 time to evaluate : 2.028 Fit side-chains REVERT: A 375 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: A 536 MET cc_start: 0.8399 (mmm) cc_final: 0.8056 (mtp) REVERT: B 139 GLU cc_start: 0.9235 (mp0) cc_final: 0.8850 (pm20) REVERT: B 144 MET cc_start: 0.8061 (tpt) cc_final: 0.7671 (tpp) REVERT: C 375 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8860 (m-30) REVERT: E 375 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8895 (m-30) REVERT: E 377 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8976 (mm-30) REVERT: E 536 MET cc_start: 0.8391 (mmm) cc_final: 0.8077 (mtp) REVERT: G 70 MET cc_start: 0.8906 (ptm) cc_final: 0.8521 (ppp) REVERT: G 364 HIS cc_start: 0.8538 (t70) cc_final: 0.8334 (t-170) REVERT: G 431 MET cc_start: 0.8984 (tpp) cc_final: 0.8695 (tpp) REVERT: G 568 MET cc_start: 0.8712 (mtt) cc_final: 0.8500 (mmm) REVERT: D 139 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8453 (pm20) REVERT: D 144 MET cc_start: 0.8054 (tpt) cc_final: 0.7690 (tpp) REVERT: F 144 MET cc_start: 0.8083 (tpt) cc_final: 0.7628 (tpt) REVERT: H 139 GLU cc_start: 0.9222 (mp0) cc_final: 0.8735 (pm20) REVERT: H 144 MET cc_start: 0.8083 (tpt) cc_final: 0.7700 (tpp) outliers start: 39 outliers final: 31 residues processed: 354 average time/residue: 0.2962 time to fit residues: 172.0281 Evaluate side-chains 337 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 303 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 644 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 40.0000 chunk 288 optimal weight: 40.0000 chunk 262 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23524 Z= 0.331 Angle : 0.665 13.143 32100 Z= 0.344 Chirality : 0.042 0.232 3788 Planarity : 0.004 0.060 4076 Dihedral : 4.176 17.375 3328 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 24.81 % Favored : 73.03 % 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: 1.03 (0.16), residues: 3088 helix: 1.57 (0.13), residues: 1860 sheet: -1.02 (0.36), residues: 204 loop : -0.53 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 517 HIS 0.008 0.001 HIS E 364 PHE 0.032 0.002 PHE G 17 TYR 0.017 0.002 TYR G 237 ARG 0.010 0.001 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 298 time to evaluate : 2.637 Fit side-chains REVERT: A 375 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: A 568 MET cc_start: 0.8952 (mtm) cc_final: 0.8507 (mmm) REVERT: B 139 GLU cc_start: 0.9306 (mp0) cc_final: 0.8925 (pm20) REVERT: B 144 MET cc_start: 0.8062 (tpt) cc_final: 0.7601 (tpt) REVERT: C 375 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: C 536 MET cc_start: 0.8336 (mmm) cc_final: 0.8131 (mtp) REVERT: E 375 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8860 (m-30) REVERT: E 377 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8924 (mm-30) REVERT: E 536 MET cc_start: 0.8443 (mmm) cc_final: 0.8122 (mtp) REVERT: G 70 MET cc_start: 0.8905 (ptm) cc_final: 0.8536 (ppp) REVERT: D 139 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8511 (pm20) REVERT: D 144 MET cc_start: 0.8084 (tpt) cc_final: 0.7642 (tpt) REVERT: F 139 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8546 (pm20) REVERT: F 144 MET cc_start: 0.8093 (tpt) cc_final: 0.7692 (tpp) REVERT: H 139 GLU cc_start: 0.9244 (mp0) cc_final: 0.8803 (pm20) REVERT: H 144 MET cc_start: 0.8064 (tpt) cc_final: 0.7588 (tpt) outliers start: 46 outliers final: 38 residues processed: 335 average time/residue: 0.2889 time to fit residues: 159.5623 Evaluate side-chains 326 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 285 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 191 optimal weight: 0.1980 chunk 151 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23524 Z= 0.203 Angle : 0.615 13.541 32100 Z= 0.310 Chirality : 0.040 0.201 3788 Planarity : 0.003 0.047 4076 Dihedral : 4.005 18.234 3328 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.78 % Allowed : 25.56 % Favored : 72.65 % 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: 1.17 (0.16), residues: 3088 helix: 1.70 (0.13), residues: 1860 sheet: -0.86 (0.37), residues: 200 loop : -0.52 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 391 HIS 0.006 0.001 HIS C 364 PHE 0.032 0.001 PHE G 17 TYR 0.017 0.001 TYR C 71 ARG 0.010 0.000 ARG G 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 307 time to evaluate : 2.594 Fit side-chains REVERT: A 375 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8835 (m-30) REVERT: A 536 MET cc_start: 0.8372 (mmm) cc_final: 0.8049 (mtp) REVERT: A 568 MET cc_start: 0.8772 (mtm) cc_final: 0.8488 (mmm) REVERT: B 139 GLU cc_start: 0.9271 (mp0) cc_final: 0.8893 (pm20) REVERT: B 144 MET cc_start: 0.8039 (tpt) cc_final: 0.7683 (tpp) REVERT: C 375 ASP cc_start: 0.9223 (OUTLIER) cc_final: 0.8881 (m-30) REVERT: E 375 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: E 377 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8982 (mm-30) REVERT: E 536 MET cc_start: 0.8448 (mmm) cc_final: 0.8145 (mtp) REVERT: E 568 MET cc_start: 0.8879 (mtm) cc_final: 0.8544 (mmm) REVERT: G 70 MET cc_start: 0.8967 (ptm) cc_final: 0.8318 (ppp) REVERT: G 431 MET cc_start: 0.8981 (tpp) cc_final: 0.8704 (tpp) REVERT: G 484 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8765 (ptp90) REVERT: D 139 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8480 (pm20) REVERT: D 144 MET cc_start: 0.8104 (tpt) cc_final: 0.7757 (tpp) REVERT: F 144 MET cc_start: 0.8100 (tpt) cc_final: 0.7742 (tpp) REVERT: H 139 GLU cc_start: 0.9252 (mp0) cc_final: 0.8750 (pm20) REVERT: H 144 MET cc_start: 0.8060 (tpt) cc_final: 0.7603 (tpt) outliers start: 38 outliers final: 33 residues processed: 339 average time/residue: 0.2925 time to fit residues: 163.9428 Evaluate side-chains 336 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 300 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.110556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092553 restraints weight = 104123.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092632 restraints weight = 77004.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.093198 restraints weight = 57615.504| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23524 Z= 0.216 Angle : 0.621 14.440 32100 Z= 0.313 Chirality : 0.040 0.207 3788 Planarity : 0.003 0.047 4076 Dihedral : 3.927 17.810 3328 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 25.89 % Favored : 72.23 % 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: 1.27 (0.16), residues: 3088 helix: 1.79 (0.13), residues: 1856 sheet: -0.83 (0.37), residues: 200 loop : -0.50 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 365 HIS 0.006 0.001 HIS E 364 PHE 0.032 0.001 PHE G 17 TYR 0.018 0.001 TYR E 71 ARG 0.009 0.000 ARG G 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.99 seconds wall clock time: 80 minutes 17.60 seconds (4817.60 seconds total)