Starting phenix.real_space_refine on Wed Feb 14 21:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2t_26319/02_2024/7u2t_26319.pdb" } resolution = 3.25 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= 0.007 sd= 0.158 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 88 5.16 5 C 6524 2.51 5 N 1728 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10300 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.75, per 1000 atoms: 0.56 Number of scatterers: 10300 At special positions: 0 Unit cell: (117.16, 117.16, 63.8, 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 88 16.00 O 1960 8.00 N 1728 7.00 C 6524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.07 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.07 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.05 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.07 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.05 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.05 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.07 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 235 " " NAG A 502 " - " ASN A 88 " " NAG B 501 " - " ASN B 235 " " NAG B 502 " - " ASN B 88 " " NAG C 501 " - " ASN C 235 " " NAG C 502 " - " ASN C 88 " " NAG D 501 " - " ASN D 235 " " NAG D 502 " - " ASN D 88 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.9% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER A 444 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU A 259 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS A 279 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 291 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS A 281 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 289 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER B 444 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU B 259 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 291 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS B 281 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 289 " --> pdb=" O CYS B 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER C 444 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU C 259 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS C 279 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 291 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS C 281 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 289 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.047A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY D 395 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 936 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: 3.21 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2811 1.33 - 1.47: 2977 1.47 - 1.60: 4648 1.60 - 1.73: 0 1.73 - 1.86: 112 Bond restraints: 10548 Sorted by residual: bond pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU D 119 " pdb=" CA GLU D 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N CYS D 281 " pdb=" CA CYS D 281 " ideal model delta sigma weight residual 1.454 1.498 -0.043 1.23e-02 6.61e+03 1.25e+01 ... (remaining 10543 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.43: 404 106.43 - 113.42: 5398 113.42 - 120.41: 4434 120.41 - 127.40: 3936 127.40 - 134.39: 124 Bond angle restraints: 14296 Sorted by residual: angle pdb=" C GLY B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY D 197 " pdb=" N PRO D 198 " pdb=" CA PRO D 198 " ideal model delta sigma weight residual 119.78 128.90 -9.12 1.03e+00 9.43e-01 7.84e+01 angle pdb=" C SER D 153 " pdb=" N PRO D 154 " pdb=" CA PRO D 154 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.65e+01 ... (remaining 14291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6008 15.12 - 30.24: 236 30.24 - 45.35: 60 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 6348 sinusoidal: 2584 harmonic: 3764 Sorted by residual: dihedral pdb=" C TYR B 402 " pdb=" N TYR B 402 " pdb=" CA TYR B 402 " pdb=" CB TYR B 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR D 402 " pdb=" N TYR D 402 " pdb=" CA TYR D 402 " pdb=" CB TYR D 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR C 402 " pdb=" N TYR C 402 " pdb=" CA TYR C 402 " pdb=" CB TYR C 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 6345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 920 0.071 - 0.142: 467 0.142 - 0.214: 121 0.214 - 0.285: 48 0.285 - 0.356: 16 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 1569 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG C 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.024 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5428 2.99 - 3.47: 8951 3.47 - 3.94: 17493 3.94 - 4.42: 20235 4.42 - 4.90: 33594 Nonbonded interactions: 85701 Sorted by model distance: nonbonded pdb=" N ASP A 416 " pdb=" OD1 ASP A 416 " model vdw 2.512 2.520 nonbonded pdb=" N ASP B 416 " pdb=" OD1 ASP B 416 " model vdw 2.512 2.520 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.512 2.520 nonbonded pdb=" N ASP D 416 " pdb=" OD1 ASP D 416 " model vdw 2.513 2.520 nonbonded pdb=" N GLN C 136 " pdb=" N GLY C 137 " model vdw 2.518 2.560 ... (remaining 85696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 2.300 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.250 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.014 0.075 10548 Z= 0.897 Angle : 1.542 9.154 14296 Z= 1.083 Chirality : 0.095 0.356 1572 Planarity : 0.013 0.222 1804 Dihedral : 10.503 75.590 3844 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 1.77 % Favored : 96.45 % Cbeta Deviations : 0.33 % 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: 0.15 (0.22), residues: 1288 helix: None (None), residues: 0 sheet: 1.06 (0.24), residues: 444 loop : -0.43 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 179 HIS 0.003 0.002 HIS D 275 PHE 0.021 0.004 PHE D 406 TYR 0.033 0.005 TYR D 276 ARG 0.005 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 1.296 Fit side-chains REVERT: A 119 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7160 (mmt90) REVERT: B 119 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7162 (mmt90) REVERT: C 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7155 (mmt90) REVERT: D 220 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7066 (mmt90) outliers start: 20 outliers final: 8 residues processed: 313 average time/residue: 0.2805 time to fit residues: 116.9585 Evaluate side-chains 185 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 185 HIS A 189 ASN A 409 HIS B 131 GLN B 185 HIS B 189 ASN B 409 HIS C 131 GLN C 185 HIS C 189 ASN C 409 HIS D 131 GLN D 185 HIS D 189 ASN D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10548 Z= 0.231 Angle : 0.585 3.868 14296 Z= 0.325 Chirality : 0.049 0.148 1572 Planarity : 0.005 0.035 1804 Dihedral : 7.140 58.943 1588 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 2.04 % Allowed : 9.75 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1288 helix: -2.48 (0.32), residues: 24 sheet: 0.90 (0.22), residues: 500 loop : 0.08 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 179 HIS 0.005 0.003 HIS D 275 PHE 0.020 0.002 PHE C 406 TYR 0.009 0.001 TYR A 316 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.146 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: A 220 ARG cc_start: 0.7533 (ttt180) cc_final: 0.7125 (mpt180) REVERT: A 361 ARG cc_start: 0.7506 (ptm-80) cc_final: 0.7212 (ptm-80) REVERT: B 220 ARG cc_start: 0.7534 (ttt180) cc_final: 0.7127 (mpt180) REVERT: B 361 ARG cc_start: 0.7505 (ptm-80) cc_final: 0.7213 (ptm-80) REVERT: C 220 ARG cc_start: 0.7532 (ttt180) cc_final: 0.7122 (mpt180) REVERT: C 361 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7218 (ptm-80) REVERT: D 220 ARG cc_start: 0.7539 (ttt180) cc_final: 0.7131 (mpt180) outliers start: 23 outliers final: 19 residues processed: 211 average time/residue: 0.2372 time to fit residues: 69.3098 Evaluate side-chains 181 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 106 optimal weight: 0.0010 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 300 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 300 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10548 Z= 0.180 Angle : 0.498 3.616 14296 Z= 0.277 Chirality : 0.047 0.143 1572 Planarity : 0.004 0.037 1804 Dihedral : 6.009 55.821 1579 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 2.84 % Allowed : 9.84 % Favored : 87.32 % 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: 0.46 (0.23), residues: 1288 helix: -2.70 (0.32), residues: 24 sheet: 0.72 (0.22), residues: 504 loop : 0.22 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 179 HIS 0.005 0.002 HIS C 275 PHE 0.014 0.002 PHE B 406 TYR 0.007 0.001 TYR C 316 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7151 (mpt180) REVERT: B 220 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7150 (mpt180) REVERT: C 220 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7144 (mpt180) REVERT: D 220 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7153 (mpt180) outliers start: 32 outliers final: 22 residues processed: 192 average time/residue: 0.2464 time to fit residues: 64.7171 Evaluate side-chains 170 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.0040 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 300 ASN B 136 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 300 ASN C 136 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 300 ASN D 136 GLN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 300 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10548 Z= 0.383 Angle : 0.590 5.310 14296 Z= 0.321 Chirality : 0.050 0.156 1572 Planarity : 0.005 0.038 1804 Dihedral : 6.314 58.301 1576 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.25 % Favored : 97.44 % Rotamer: Outliers : 3.55 % Allowed : 12.15 % Favored : 84.31 % 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: 0.07 (0.23), residues: 1288 helix: -3.45 (0.20), residues: 24 sheet: 0.50 (0.22), residues: 548 loop : -0.11 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 179 HIS 0.007 0.003 HIS D 185 PHE 0.022 0.003 PHE A 406 TYR 0.009 0.001 TYR A 353 ARG 0.007 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8507 (mm-40) REVERT: A 220 ARG cc_start: 0.7653 (ttt180) cc_final: 0.7143 (mpt180) REVERT: A 376 ASP cc_start: 0.7226 (t0) cc_final: 0.6807 (t0) REVERT: A 380 TRP cc_start: 0.8380 (t-100) cc_final: 0.8178 (t-100) REVERT: B 118 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7951 (ptm-80) REVERT: B 220 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7144 (mpt180) REVERT: B 376 ASP cc_start: 0.7220 (t0) cc_final: 0.6807 (t0) REVERT: B 380 TRP cc_start: 0.8408 (t-100) cc_final: 0.8193 (t-100) REVERT: C 136 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8501 (mm-40) REVERT: C 175 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 220 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7137 (mpt180) REVERT: C 376 ASP cc_start: 0.7221 (t0) cc_final: 0.6808 (t0) REVERT: C 380 TRP cc_start: 0.8404 (t-100) cc_final: 0.8187 (t-100) REVERT: D 136 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8517 (mm-40) REVERT: D 175 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8147 (mm-30) REVERT: D 220 ARG cc_start: 0.7652 (ttt180) cc_final: 0.7146 (mpt180) REVERT: D 376 ASP cc_start: 0.7245 (t0) cc_final: 0.6826 (t0) REVERT: D 380 TRP cc_start: 0.8402 (t-100) cc_final: 0.8192 (t-100) outliers start: 40 outliers final: 25 residues processed: 198 average time/residue: 0.2569 time to fit residues: 68.9636 Evaluate side-chains 182 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 136 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN C 136 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN D 136 GLN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10548 Z= 0.239 Angle : 0.504 3.770 14296 Z= 0.277 Chirality : 0.047 0.148 1572 Planarity : 0.004 0.039 1804 Dihedral : 6.055 56.283 1576 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.01 % Favored : 98.68 % Rotamer: Outliers : 3.63 % Allowed : 12.15 % Favored : 84.22 % 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: 0.03 (0.23), residues: 1288 helix: -3.06 (0.26), residues: 24 sheet: 0.51 (0.22), residues: 528 loop : -0.17 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 179 HIS 0.005 0.002 HIS A 275 PHE 0.016 0.002 PHE A 406 TYR 0.008 0.001 TYR C 316 ARG 0.004 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6885 (m-30) REVERT: A 186 ASP cc_start: 0.8475 (p0) cc_final: 0.8255 (p0) REVERT: A 220 ARG cc_start: 0.7596 (ttt180) cc_final: 0.7131 (mpt180) REVERT: A 376 ASP cc_start: 0.7310 (t0) cc_final: 0.6887 (t0) REVERT: B 142 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: B 186 ASP cc_start: 0.8476 (p0) cc_final: 0.8259 (p0) REVERT: B 220 ARG cc_start: 0.7598 (ttt180) cc_final: 0.7130 (mpt180) REVERT: B 376 ASP cc_start: 0.7310 (t0) cc_final: 0.6888 (t0) REVERT: C 142 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 186 ASP cc_start: 0.8526 (p0) cc_final: 0.8321 (p0) REVERT: C 220 ARG cc_start: 0.7594 (ttt180) cc_final: 0.7128 (mpt180) REVERT: C 376 ASP cc_start: 0.7307 (t0) cc_final: 0.6889 (t0) REVERT: D 142 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: D 186 ASP cc_start: 0.8480 (p0) cc_final: 0.8261 (p0) REVERT: D 220 ARG cc_start: 0.7596 (ttt180) cc_final: 0.7137 (mpt180) REVERT: D 376 ASP cc_start: 0.7250 (t0) cc_final: 0.6834 (t0) outliers start: 41 outliers final: 29 residues processed: 185 average time/residue: 0.2403 time to fit residues: 62.1070 Evaluate side-chains 195 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10548 Z= 0.200 Angle : 0.479 3.745 14296 Z= 0.263 Chirality : 0.047 0.146 1572 Planarity : 0.004 0.039 1804 Dihedral : 5.881 55.287 1576 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.09 % Favored : 98.60 % Rotamer: Outliers : 3.55 % Allowed : 12.50 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1288 helix: -2.81 (0.30), residues: 24 sheet: 0.46 (0.22), residues: 528 loop : -0.13 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 179 HIS 0.003 0.001 HIS B 275 PHE 0.015 0.002 PHE A 406 TYR 0.007 0.001 TYR C 316 ARG 0.004 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7613 (ttt180) cc_final: 0.7136 (mpt180) REVERT: A 376 ASP cc_start: 0.7440 (t0) cc_final: 0.7031 (t0) REVERT: B 220 ARG cc_start: 0.7592 (ttt180) cc_final: 0.7134 (mpt180) REVERT: B 376 ASP cc_start: 0.7445 (t0) cc_final: 0.7037 (t0) REVERT: C 220 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7135 (mpt180) REVERT: C 376 ASP cc_start: 0.7444 (t0) cc_final: 0.7032 (t0) REVERT: D 220 ARG cc_start: 0.7616 (ttt180) cc_final: 0.7141 (mpt180) REVERT: D 376 ASP cc_start: 0.7472 (t0) cc_final: 0.7053 (t0) outliers start: 40 outliers final: 28 residues processed: 181 average time/residue: 0.2383 time to fit residues: 60.3279 Evaluate side-chains 182 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10548 Z= 0.357 Angle : 0.553 4.544 14296 Z= 0.300 Chirality : 0.049 0.154 1572 Planarity : 0.005 0.040 1804 Dihedral : 6.190 57.979 1576 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.18 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 13.30 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1288 helix: -3.32 (0.20), residues: 24 sheet: 0.03 (0.21), residues: 556 loop : -0.18 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 179 HIS 0.008 0.003 HIS D 185 PHE 0.021 0.003 PHE B 406 TYR 0.007 0.001 TYR D 353 ARG 0.004 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7510 (ttt180) cc_final: 0.7012 (mpt180) REVERT: A 227 GLN cc_start: 0.8911 (mt0) cc_final: 0.8676 (mt0) REVERT: A 376 ASP cc_start: 0.7384 (t0) cc_final: 0.6966 (t0) REVERT: B 220 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7015 (mpt180) REVERT: B 227 GLN cc_start: 0.8909 (mt0) cc_final: 0.8677 (mt0) REVERT: B 376 ASP cc_start: 0.7379 (t0) cc_final: 0.6963 (t0) REVERT: C 220 ARG cc_start: 0.7513 (ttt180) cc_final: 0.7011 (mpt180) REVERT: C 376 ASP cc_start: 0.7382 (t0) cc_final: 0.6970 (t0) REVERT: D 220 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7017 (mpt180) REVERT: D 376 ASP cc_start: 0.7392 (t0) cc_final: 0.6970 (t0) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.2701 time to fit residues: 65.9918 Evaluate side-chains 176 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10548 Z= 0.243 Angle : 0.497 3.789 14296 Z= 0.272 Chirality : 0.048 0.147 1572 Planarity : 0.005 0.039 1804 Dihedral : 5.984 56.262 1576 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.63 % Favored : 98.06 % Rotamer: Outliers : 2.57 % Allowed : 13.48 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1288 helix: -2.99 (0.25), residues: 24 sheet: 0.10 (0.21), residues: 528 loop : -0.26 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 179 HIS 0.005 0.002 HIS C 275 PHE 0.016 0.002 PHE D 121 TYR 0.005 0.001 TYR B 316 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7011 (mpt180) REVERT: A 227 GLN cc_start: 0.8911 (mt0) cc_final: 0.8690 (mt0) REVERT: A 376 ASP cc_start: 0.7533 (t0) cc_final: 0.7105 (t0) REVERT: B 220 ARG cc_start: 0.7497 (ttt180) cc_final: 0.7013 (mpt180) REVERT: B 227 GLN cc_start: 0.8891 (mt0) cc_final: 0.8676 (mt0) REVERT: B 376 ASP cc_start: 0.7526 (t0) cc_final: 0.7104 (t0) REVERT: C 220 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7012 (mpt180) REVERT: C 376 ASP cc_start: 0.7533 (t0) cc_final: 0.7106 (t0) REVERT: D 220 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7023 (mpt180) REVERT: D 376 ASP cc_start: 0.7520 (t0) cc_final: 0.7089 (t0) outliers start: 29 outliers final: 26 residues processed: 164 average time/residue: 0.2409 time to fit residues: 54.7520 Evaluate side-chains 178 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10548 Z= 0.186 Angle : 0.467 3.685 14296 Z= 0.255 Chirality : 0.047 0.145 1572 Planarity : 0.004 0.038 1804 Dihedral : 5.817 55.588 1576 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.94 % Favored : 97.75 % Rotamer: Outliers : 2.30 % Allowed : 13.92 % Favored : 83.78 % 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: -0.26 (0.23), residues: 1288 helix: -2.82 (0.28), residues: 24 sheet: 0.15 (0.22), residues: 528 loop : -0.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.004 0.002 HIS D 275 PHE 0.013 0.002 PHE D 121 TYR 0.006 0.001 TYR D 316 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7710 (ttt180) cc_final: 0.6961 (mpt180) REVERT: A 227 GLN cc_start: 0.8886 (mt0) cc_final: 0.8678 (mt0) REVERT: A 376 ASP cc_start: 0.7539 (t0) cc_final: 0.7124 (t0) REVERT: B 220 ARG cc_start: 0.7717 (ttt180) cc_final: 0.6958 (mpt180) REVERT: B 376 ASP cc_start: 0.7533 (t0) cc_final: 0.7120 (t0) REVERT: C 220 ARG cc_start: 0.7708 (ttt180) cc_final: 0.6960 (mpt180) REVERT: C 376 ASP cc_start: 0.7536 (t0) cc_final: 0.7125 (t0) REVERT: C 398 GLU cc_start: 0.7067 (tp30) cc_final: 0.6367 (tt0) REVERT: D 220 ARG cc_start: 0.7716 (ttt180) cc_final: 0.6953 (mpt180) REVERT: D 376 ASP cc_start: 0.7531 (t0) cc_final: 0.7116 (t0) outliers start: 26 outliers final: 22 residues processed: 178 average time/residue: 0.2517 time to fit residues: 60.9616 Evaluate side-chains 183 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10548 Z= 0.353 Angle : 0.548 4.064 14296 Z= 0.297 Chirality : 0.049 0.152 1572 Planarity : 0.005 0.037 1804 Dihedral : 6.132 58.353 1576 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Rotamer: Outliers : 2.30 % Allowed : 14.27 % Favored : 83.42 % 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: -0.32 (0.23), residues: 1288 helix: -3.31 (0.18), residues: 24 sheet: 0.05 (0.22), residues: 556 loop : -0.21 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 179 HIS 0.005 0.002 HIS D 275 PHE 0.020 0.003 PHE B 406 TYR 0.006 0.001 TYR A 353 ARG 0.008 0.001 ARG D 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.6897 (mtm-85) REVERT: A 220 ARG cc_start: 0.7752 (ttt180) cc_final: 0.6958 (mpt180) REVERT: A 227 GLN cc_start: 0.8884 (mt0) cc_final: 0.8656 (mt0) REVERT: A 376 ASP cc_start: 0.7599 (t0) cc_final: 0.7151 (t0) REVERT: B 152 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7042 (mtm-85) REVERT: B 220 ARG cc_start: 0.7752 (ttt180) cc_final: 0.6964 (mpt180) REVERT: B 376 ASP cc_start: 0.7590 (t0) cc_final: 0.7150 (t0) REVERT: C 152 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: C 220 ARG cc_start: 0.7747 (ttt180) cc_final: 0.6950 (mpt180) REVERT: C 376 ASP cc_start: 0.7595 (t0) cc_final: 0.7150 (t0) REVERT: D 152 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.6886 (mtm-85) REVERT: D 220 ARG cc_start: 0.7748 (ttt180) cc_final: 0.6956 (mpt180) REVERT: D 376 ASP cc_start: 0.7594 (t0) cc_final: 0.7139 (t0) outliers start: 26 outliers final: 24 residues processed: 181 average time/residue: 0.2800 time to fit residues: 67.2657 Evaluate side-chains 192 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 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 = 0.3610 r_free = 0.3610 target = 0.149713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118733 restraints weight = 11359.166| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10548 Z= 0.180 Angle : 0.477 3.888 14296 Z= 0.262 Chirality : 0.047 0.148 1572 Planarity : 0.005 0.038 1804 Dihedral : 5.867 55.654 1576 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.79 % Favored : 97.90 % Rotamer: Outliers : 2.30 % Allowed : 14.18 % Favored : 83.51 % 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: -0.30 (0.23), residues: 1288 helix: -3.05 (0.22), residues: 24 sheet: 0.11 (0.22), residues: 528 loop : -0.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 179 HIS 0.005 0.002 HIS B 275 PHE 0.014 0.002 PHE C 121 TYR 0.006 0.001 TYR B 316 ARG 0.006 0.000 ARG D 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.40 seconds wall clock time: 44 minutes 36.20 seconds (2676.20 seconds total)