Starting phenix.real_space_refine (version: dev) on Tue Apr 5 23:16:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/04_2022/6y1z_10673_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E ARG 439": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 16610 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "D" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "B" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "C" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "E" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 127 Unusual residues: {'BMA': 1, 'NAG': 5, 'O7B': 1} Classifications: {'undetermined': 7, 'peptide': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="HIS A 502 " pdbres="NAG A 503 " Not linked: pdbres="NAG A 503 " pdbres="BMA A 504 " Not linked: pdbres="BMA A 504 " pdbres="NAG A 505 " Not linked: pdbres="NAG A 505 " pdbres="NAG A 506 " Not linked: pdbres="NAG A 506 " pdbres="NAG A 507 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 127 Unusual residues: {'BMA': 1, 'NAG': 5, 'O7B': 1} Classifications: {'undetermined': 7, 'peptide': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="HIS D 502 " pdbres="NAG D 503 " Not linked: pdbres="NAG D 503 " pdbres="BMA D 504 " Not linked: pdbres="BMA D 504 " pdbres="NAG D 505 " Not linked: pdbres="NAG D 505 " pdbres="NAG D 506 " Not linked: pdbres="NAG D 506 " pdbres="NAG D 507 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 127 Unusual residues: {'BMA': 1, 'NAG': 5, 'O7B': 1} Classifications: {'undetermined': 7, 'peptide': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="HIS B 502 " pdbres="NAG B 503 " Not linked: pdbres="NAG B 503 " pdbres="BMA B 504 " Not linked: pdbres="BMA B 504 " pdbres="NAG B 505 " Not linked: pdbres="NAG B 505 " pdbres="NAG B 506 " Not linked: pdbres="NAG B 506 " pdbres="NAG B 507 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 127 Unusual residues: {'BMA': 1, 'NAG': 5, 'O7B': 1} Classifications: {'undetermined': 7, 'peptide': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="O7B C 501 " pdbres="TRP C 502 " Not linked: pdbres="HIS C 503 " pdbres="NAG C 504 " Not linked: pdbres="NAG C 504 " pdbres="BMA C 505 " Not linked: pdbres="BMA C 505 " pdbres="NAG C 506 " Not linked: pdbres="NAG C 506 " pdbres="NAG C 507 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 127 Unusual residues: {'BMA': 1, 'NAG': 5, 'O7B': 1} Classifications: {'undetermined': 7, 'peptide': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="O7B E 501 " pdbres="TRP E 502 " Not linked: pdbres="HIS E 503 " pdbres="NAG E 504 " Not linked: pdbres="NAG E 504 " pdbres="BMA E 505 " Not linked: pdbres="BMA E 505 " pdbres="NAG E 506 " Not linked: pdbres="NAG E 506 " pdbres="NAG E 507 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ATYR A 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 67 " occ=0.50 residue: pdb=" N ATRP A 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 168 " occ=0.50 residue: pdb=" N ATYR D 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 67 " occ=0.50 residue: pdb=" N ATRP D 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP D 168 " occ=0.50 residue: pdb=" N ATYR B 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 67 " occ=0.50 residue: pdb=" N ATRP B 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 168 " occ=0.50 residue: pdb=" N ATYR C 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 67 " occ=0.50 residue: pdb=" N ATRP C 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP C 168 " occ=0.50 residue: pdb=" N ATYR E 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 67 " occ=0.50 residue: pdb=" N ATRP E 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP E 168 " occ=0.50 Time building chain proxies: 19.13, per 1000 atoms: 1.15 Number of scatterers: 16610 At special positions: 0 Unit cell: (101.365, 103.499, 168.586, 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 45 16.00 O 2960 8.00 N 2670 7.00 C 10935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BMA A 504 " - " NAG A 505 " " NAG A 505 " - " NAG A 506 " " NAG A 507 " - " NAG A 508 " " BMA B 504 " - " NAG B 505 " " NAG B 505 " - " NAG B 506 " " NAG B 507 " - " NAG B 508 " " BMA C 505 " - " NAG C 506 " " NAG C 506 " - " NAG C 507 " " NAG C 508 " - " NAG C 509 " " BMA D 504 " - " NAG D 505 " " NAG D 505 " - " NAG D 506 " " NAG D 507 " - " NAG D 508 " " BMA E 505 " - " NAG E 506 " " NAG E 506 " - " NAG E 507 " " NAG E 508 " - " NAG E 509 " NAG-ASN " NAG A 503 " - " ASN A 82 " " NAG A 506 " - " ASN A 164 " " NAG A 507 " - " ASN A 148 " " NAG B 503 " - " ASN B 82 " " NAG B 506 " - " ASN B 164 " " NAG B 507 " - " ASN B 148 " " NAG C 504 " - " ASN C 82 " " NAG C 507 " - " ASN C 164 " " NAG C 508 " - " ASN C 148 " " NAG D 503 " - " ASN D 82 " " NAG D 506 " - " ASN D 164 " " NAG D 507 " - " ASN D 148 " " NAG E 504 " - " ASN E 82 " " NAG E 507 " - " ASN E 164 " " NAG E 508 " - " ASN E 148 " Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 4.8 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL A 225 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.742A pdb=" N PHE A 242 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 283 through 308 Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 398 through 457 Processing helix chain 'D' and resid 13 through 20 Processing helix chain 'D' and resid 77 through 80 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL D 225 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU D 228 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU D 229 " --> pdb=" O SER D 226 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.742A pdb=" N PHE D 242 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 269 Processing helix chain 'D' and resid 283 through 308 Processing helix chain 'D' and resid 319 through 328 Processing helix chain 'D' and resid 398 through 457 Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 77 through 80 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU B 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.741A pdb=" N PHE B 242 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 283 through 308 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 398 through 457 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 220 through 243 removed outlier: 3.647A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL C 225 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 229 " --> pdb=" O SER C 226 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.741A pdb=" N PHE C 242 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 269 Processing helix chain 'C' and resid 283 through 308 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 398 through 457 Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 77 through 80 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 220 through 243 removed outlier: 3.647A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL E 225 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 228 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU E 229 " --> pdb=" O SER E 226 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 3.742A pdb=" N PHE E 242 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 269 Processing helix chain 'E' and resid 283 through 308 Processing helix chain 'E' and resid 319 through 328 Processing helix chain 'E' and resid 398 through 457 Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.108A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.117A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.115A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.108A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2255 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: 6.28 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4239 1.33 - 1.45: 3326 1.45 - 1.57: 9450 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17085 Sorted by residual: bond pdb=" C18 O7B C 501 " pdb=" C19 O7B C 501 " ideal model delta sigma weight residual 1.725 1.520 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C18 O7B B 509 " pdb=" C19 O7B B 509 " ideal model delta sigma weight residual 1.725 1.520 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C18 O7B A 509 " pdb=" C19 O7B A 509 " ideal model delta sigma weight residual 1.725 1.520 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C18 O7B D 509 " pdb=" C19 O7B D 509 " ideal model delta sigma weight residual 1.725 1.521 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C18 O7B E 501 " pdb=" C19 O7B E 501 " ideal model delta sigma weight residual 1.725 1.521 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 17080 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.27: 704 107.27 - 113.96: 10006 113.96 - 120.66: 6753 120.66 - 127.35: 5644 127.35 - 134.05: 258 Bond angle restraints: 23365 Sorted by residual: angle pdb=" C04 O7B C 501 " pdb=" N05 O7B C 501 " pdb=" C06 O7B C 501 " ideal model delta sigma weight residual 110.83 120.69 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C04 O7B D 509 " pdb=" N05 O7B D 509 " pdb=" C06 O7B D 509 " ideal model delta sigma weight residual 110.83 120.67 -9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C04 O7B A 509 " pdb=" N05 O7B A 509 " pdb=" C06 O7B A 509 " ideal model delta sigma weight residual 110.83 120.66 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C04 O7B E 501 " pdb=" N05 O7B E 501 " pdb=" C06 O7B E 501 " ideal model delta sigma weight residual 110.83 120.61 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C04 O7B B 509 " pdb=" N05 O7B B 509 " pdb=" C06 O7B B 509 " ideal model delta sigma weight residual 110.83 120.59 -9.76 3.00e+00 1.11e-01 1.06e+01 ... (remaining 23360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 9577 23.20 - 46.40: 343 46.40 - 69.60: 40 69.60 - 92.80: 25 92.80 - 116.00: 20 Dihedral angle restraints: 10005 sinusoidal: 4210 harmonic: 5795 Sorted by residual: dihedral pdb=" C2 NAG C 509 " pdb=" C3 NAG C 509 " pdb=" C4 NAG C 509 " pdb=" C5 NAG C 509 " ideal model delta sinusoidal sigma weight residual 50.00 -53.83 103.83 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" C2 NAG B 508 " pdb=" C3 NAG B 508 " pdb=" C4 NAG B 508 " pdb=" C5 NAG B 508 " ideal model delta sinusoidal sigma weight residual 50.00 -53.80 103.80 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" C2 NAG A 508 " pdb=" C3 NAG A 508 " pdb=" C4 NAG A 508 " pdb=" C5 NAG A 508 " ideal model delta sinusoidal sigma weight residual 50.00 -53.79 103.79 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 10002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.097: 2770 1.097 - 2.194: 0 2.194 - 3.291: 0 3.291 - 4.388: 0 4.388 - 5.485: 5 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C20 O7B C 501 " pdb=" C15 O7B C 501 " pdb=" C19 O7B C 501 " pdb=" C21 O7B C 501 " both_signs ideal model delta sigma weight residual False 2.72 -2.77 5.49 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C20 O7B D 509 " pdb=" C15 O7B D 509 " pdb=" C19 O7B D 509 " pdb=" C21 O7B D 509 " both_signs ideal model delta sigma weight residual False 2.72 -2.77 5.48 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C20 O7B B 509 " pdb=" C15 O7B B 509 " pdb=" C19 O7B B 509 " pdb=" C21 O7B B 509 " both_signs ideal model delta sigma weight residual False 2.72 -2.77 5.48 2.00e-01 2.50e+01 7.52e+02 ... (remaining 2772 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 O7B E 501 " -0.020 2.00e-02 2.50e+03 1.51e-02 3.42e+00 pdb=" C06 O7B E 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B E 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B E 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B E 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B E 501 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B D 509 " -0.020 2.00e-02 2.50e+03 1.50e-02 3.37e+00 pdb=" C06 O7B D 509 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B D 509 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B D 509 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B D 509 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B D 509 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B C 501 " -0.020 2.00e-02 2.50e+03 1.48e-02 3.30e+00 pdb=" C06 O7B C 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B C 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B C 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B C 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B C 501 " -0.022 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5148 2.84 - 3.36: 14896 3.36 - 3.87: 27346 3.87 - 4.39: 30193 4.39 - 4.90: 54117 Nonbonded interactions: 131700 Sorted by model distance: nonbonded pdb=" OD1 ASP D 105 " pdb=" N VAL D 106 " model vdw 2.325 2.520 nonbonded pdb=" OD1 ASP B 105 " pdb=" N VAL B 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP E 105 " pdb=" N VAL E 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP A 105 " pdb=" N VAL A 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP C 105 " pdb=" N VAL C 106 " model vdw 2.326 2.520 ... (remaining 131695 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' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458 or resid 506 through 508)) selection = (chain 'B' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458 or resid 506 through 508)) selection = (chain 'C' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458 or resid 506 through 508)) selection = (chain 'D' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458 or resid 506 through 508)) selection = (chain 'E' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458 or resid 506 through 508)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10935 2.51 5 N 2670 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 0.010 Normalize map: mean=0, sd=1: 2.950 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: 0.000 Extract box with map and model: 7.470 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.150 Process input model: 62.460 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:18.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.205 17085 Z= 0.429 Angle : 0.616 9.865 23365 Z= 0.303 Chirality : 0.237 5.485 2775 Planarity : 0.003 0.034 2820 Dihedral : 14.026 115.997 6220 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 1930 helix: 1.38 (0.18), residues: 745 sheet: -2.65 (0.18), residues: 470 loop : -2.08 (0.21), residues: 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 237 average time/residue: 1.2213 time to fit residues: 328.7687 Evaluate side-chains 124 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0570 chunk 144 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 66 GLN A 125 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN B 101 ASN B 125 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 55 ASN C 111 ASN C 125 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 55 ASN E 66 GLN E 125 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 17085 Z= 0.195 Angle : 0.856 22.041 23365 Z= 0.353 Chirality : 0.126 2.787 2775 Planarity : 0.005 0.053 2820 Dihedral : 12.451 104.545 2395 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 3.20 % 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: -0.39 (0.19), residues: 1930 helix: 2.19 (0.19), residues: 745 sheet: -2.25 (0.20), residues: 480 loop : -1.42 (0.23), residues: 705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 112 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 24 residues processed: 153 average time/residue: 1.0296 time to fit residues: 181.0929 Evaluate side-chains 120 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 4 average time/residue: 0.1773 time to fit residues: 3.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 55 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 111 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17085 Z= 0.222 Angle : 0.848 22.024 23365 Z= 0.346 Chirality : 0.123 2.714 2775 Planarity : 0.004 0.038 2820 Dihedral : 12.453 104.534 2395 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1930 helix: 2.49 (0.18), residues: 740 sheet: -1.89 (0.20), residues: 480 loop : -1.00 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 111 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 154 average time/residue: 1.0020 time to fit residues: 178.6270 Evaluate side-chains 127 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 6 average time/residue: 0.1917 time to fit residues: 4.8545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 55 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN B 55 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 50 ASN C 111 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 17085 Z= 0.237 Angle : 0.852 22.133 23365 Z= 0.348 Chirality : 0.123 2.701 2775 Planarity : 0.005 0.074 2820 Dihedral : 12.469 104.516 2395 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1930 helix: 2.63 (0.18), residues: 740 sheet: -1.73 (0.21), residues: 480 loop : -0.81 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 109 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 47 residues processed: 155 average time/residue: 0.9267 time to fit residues: 166.7127 Evaluate side-chains 143 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 96 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 6 average time/residue: 0.1713 time to fit residues: 4.4634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN B 55 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 111 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 50 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 17085 Z= 0.185 Angle : 0.833 22.080 23365 Z= 0.337 Chirality : 0.122 2.704 2775 Planarity : 0.004 0.069 2820 Dihedral : 12.424 104.499 2395 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 3.48 % 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: 0.60 (0.20), residues: 1930 helix: 2.85 (0.18), residues: 740 sheet: -1.82 (0.20), residues: 530 loop : -0.43 (0.25), residues: 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 100 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 45 residues processed: 151 average time/residue: 0.9928 time to fit residues: 173.4227 Evaluate side-chains 141 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 4 average time/residue: 0.1743 time to fit residues: 3.8981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 22 ASN B 55 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 17085 Z= 0.228 Angle : 0.841 22.183 23365 Z= 0.341 Chirality : 0.122 2.692 2775 Planarity : 0.004 0.046 2820 Dihedral : 12.453 104.606 2395 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1930 helix: 2.90 (0.18), residues: 740 sheet: -1.73 (0.20), residues: 530 loop : -0.33 (0.25), residues: 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 98 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 45 residues processed: 150 average time/residue: 0.9633 time to fit residues: 167.7671 Evaluate side-chains 141 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 5 average time/residue: 0.1845 time to fit residues: 4.3797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 22 ASN B 55 ASN B 314 GLN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17085 Z= 0.178 Angle : 0.825 22.161 23365 Z= 0.332 Chirality : 0.122 2.694 2775 Planarity : 0.004 0.038 2820 Dihedral : 12.399 104.511 2395 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1930 helix: 3.06 (0.18), residues: 740 sheet: -1.57 (0.21), residues: 505 loop : -0.28 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 105 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 43 residues processed: 149 average time/residue: 0.9965 time to fit residues: 171.3541 Evaluate side-chains 140 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 97 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 40 residues processed: 4 average time/residue: 0.2144 time to fit residues: 4.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 55 ASN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.198 17085 Z= 0.216 Angle : 0.851 22.197 23365 Z= 0.348 Chirality : 0.122 2.685 2775 Planarity : 0.004 0.065 2820 Dihedral : 12.427 104.460 2395 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1930 helix: 2.98 (0.18), residues: 740 sheet: -1.38 (0.22), residues: 480 loop : -0.26 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 100 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 46 residues processed: 143 average time/residue: 1.0298 time to fit residues: 170.1633 Evaluate side-chains 143 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 97 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 6 average time/residue: 0.1917 time to fit residues: 4.5905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 22 ASN B 55 ASN B 314 GLN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 17085 Z= 0.197 Angle : 0.846 22.194 23365 Z= 0.342 Chirality : 0.121 2.681 2775 Planarity : 0.004 0.055 2820 Dihedral : 12.414 104.529 2395 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1930 helix: 3.05 (0.18), residues: 740 sheet: -1.31 (0.22), residues: 480 loop : -0.20 (0.25), residues: 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 106 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 42 residues processed: 152 average time/residue: 0.9879 time to fit residues: 174.0855 Evaluate side-chains 139 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 2 average time/residue: 0.1998 time to fit residues: 3.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 174 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 22 ASN B 55 ASN B 314 GLN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 17085 Z= 0.203 Angle : 0.845 22.167 23365 Z= 0.344 Chirality : 0.121 2.676 2775 Planarity : 0.004 0.052 2820 Dihedral : 12.423 104.594 2395 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1930 helix: 2.73 (0.18), residues: 765 sheet: -1.28 (0.22), residues: 480 loop : -0.11 (0.25), residues: 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 42 residues processed: 141 average time/residue: 1.0860 time to fit residues: 175.8187 Evaluate side-chains 137 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 2 average time/residue: 0.1857 time to fit residues: 3.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 55 ASN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.083787 restraints weight = 77325.459| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.95 r_work: 0.2953 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work: 0.2921 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work: 0.2905 rms_B_bonded: 4.57 restraints_weight: 0.0625 r_work: 0.2889 rms_B_bonded: 4.63 restraints_weight: 0.0312 r_work: 0.2873 rms_B_bonded: 4.71 restraints_weight: 0.0156 r_work: 0.2857 rms_B_bonded: 4.82 restraints_weight: 0.0078 r_work: 0.2841 rms_B_bonded: 4.94 restraints_weight: 0.0039 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17085 Z= 0.186 Angle : 0.851 22.155 23365 Z= 0.343 Chirality : 0.121 2.675 2775 Planarity : 0.004 0.048 2820 Dihedral : 12.395 104.575 2395 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1930 helix: 2.79 (0.19), residues: 765 sheet: -1.20 (0.22), residues: 475 loop : -0.08 (0.25), residues: 690 =============================================================================== Job complete usr+sys time: 3989.60 seconds wall clock time: 73 minutes 29.14 seconds (4409.14 seconds total)