Starting phenix.real_space_refine on Tue Dec 31 21:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.map" model { file = "/net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pc0_13315/12_2024/7pc0_13315.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 893 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 104 5.16 5 C 10181 2.51 5 N 2582 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15748 Number of models: 1 Model: "" Number of chains: 17 Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2695 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 518 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 497 Classifications: {'peptide': 67} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 5, 'TRANS': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" 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: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' ZN': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'HEX': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.38, per 1000 atoms: 0.66 Number of scatterers: 15748 At special positions: 0 Unit cell: (97.11, 137.78, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 104 16.00 O 2880 8.00 N 2582 7.00 C 10181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS K 3 " - pdb=" SG CYS K 20 " distance=2.03 Simple disulfide: pdb=" SG CYS K 3 " - pdb=" SG CYS K 62 " distance=2.05 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS K 41 " distance=2.03 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS K 57 " distance=2.06 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS K 62 " distance=2.02 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 30 " distance=2.04 Simple disulfide: pdb=" SG CYS K 45 " - pdb=" SG CYS K 56 " distance=2.04 Simple disulfide: pdb=" SG CYS K 57 " - pdb=" SG CYS K 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 20 " distance=2.03 Simple disulfide: pdb=" SG CYS L 14 " - pdb=" SG CYS L 41 " distance=2.04 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 57 " distance=2.05 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 57 " - pdb=" SG CYS L 62 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 4 " - " MAN G 6 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG C 501 " - " ASN C 80 " " NAG E 501 " - " ASN E 80 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN E 149 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 267 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS E 267 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS C 267 " 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 37.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'F' and resid 414 through 418 Processing helix chain 'F' and resid 448 through 452 Processing helix chain 'F' and resid 474 through 478 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'A' and resid 13 through 23 removed outlier: 4.182A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.370A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.996A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 248 Proline residue: A 233 - end of helix removed outlier: 4.570A pdb=" N ASN A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 277 Processing helix chain 'A' and resid 286 through 310 removed outlier: 3.611A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 415 removed outlier: 3.545A pdb=" N ALA A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.563A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 220 through 242 Proline residue: B 228 - end of helix removed outlier: 3.634A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 420 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.542A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.890A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 420 through 446 Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 220 through 239 removed outlier: 4.342A pdb=" N GLN E 224 " --> pdb=" O TYR E 220 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.698A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 Processing helix chain 'E' and resid 420 through 446 Proline residue: E 432 - end of helix Processing helix chain 'D' and resid 13 through 23 removed outlier: 4.112A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.332A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.911A pdb=" N VAL D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.568A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 418 removed outlier: 3.651A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.838A pdb=" N ARG D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 70 removed outlier: 3.789A pdb=" N LYS K 69 " --> pdb=" O PRO K 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 420 through 426 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 446 current: chain 'F' and resid 501 through 502 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 54 removed outlier: 6.374A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.241A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A 210 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 202 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 212 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A 200 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR A 214 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 198 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS A 216 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN A 196 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A 218 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 51 removed outlier: 6.435A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU B 125 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.310A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.345A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.176A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 6.498A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.267A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 47 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 47 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.281A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 25 637 hydrogen bonds defined for protein. 1797 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: 4.47 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4852 1.35 - 1.48: 4506 1.48 - 1.61: 6622 1.61 - 1.73: 0 1.73 - 1.86: 166 Bond restraints: 16146 Sorted by residual: bond pdb=" CG HSM B 601 " pdb=" ND1 HSM B 601 " ideal model delta sigma weight residual 1.383 1.314 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CD2 HSM B 601 " pdb=" NE2 HSM B 601 " ideal model delta sigma weight residual 1.376 1.314 0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 16141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21422 2.07 - 4.13: 411 4.13 - 6.20: 99 6.20 - 8.26: 13 8.26 - 10.33: 4 Bond angle restraints: 21949 Sorted by residual: angle pdb=" CA THR L 6 " pdb=" CB THR L 6 " pdb=" CG2 THR L 6 " ideal model delta sigma weight residual 110.50 119.61 -9.11 1.70e+00 3.46e-01 2.87e+01 angle pdb=" OG1 THR L 6 " pdb=" CB THR L 6 " pdb=" CG2 THR L 6 " ideal model delta sigma weight residual 109.30 119.63 -10.33 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N THR K 6 " pdb=" CA THR K 6 " pdb=" C THR K 6 " ideal model delta sigma weight residual 109.81 119.93 -10.12 2.21e+00 2.05e-01 2.10e+01 angle pdb=" CA THR L 6 " pdb=" CB THR L 6 " pdb=" OG1 THR L 6 " ideal model delta sigma weight residual 109.60 115.25 -5.65 1.50e+00 4.44e-01 1.42e+01 angle pdb=" CA CYS K 62 " pdb=" CB CYS K 62 " pdb=" SG CYS K 62 " ideal model delta sigma weight residual 114.40 121.91 -7.51 2.30e+00 1.89e-01 1.07e+01 ... (remaining 21944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 9346 25.75 - 51.50: 398 51.50 - 77.24: 44 77.24 - 102.99: 26 102.99 - 128.74: 17 Dihedral angle restraints: 9831 sinusoidal: 4210 harmonic: 5621 Sorted by residual: dihedral pdb=" CB CYS K 20 " pdb=" SG CYS K 20 " pdb=" SG CYS K 62 " pdb=" CB CYS K 62 " ideal model delta sinusoidal sigma weight residual 93.00 -178.78 -88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS L 20 " pdb=" SG CYS L 20 " pdb=" SG CYS L 57 " pdb=" CB CYS L 57 " ideal model delta sinusoidal sigma weight residual -86.00 -1.98 -84.02 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS L 14 " pdb=" SG CYS L 14 " pdb=" SG CYS L 41 " pdb=" CB CYS L 41 " ideal model delta sinusoidal sigma weight residual 93.00 171.60 -78.60 1 1.00e+01 1.00e-02 7.70e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.042: 2523 1.042 - 2.085: 7 2.085 - 3.127: 2 3.127 - 4.169: 3 4.169 - 5.212: 2 Chirality restraints: 2537 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 -2.81 5.21 2.00e-02 2.50e+03 6.79e+04 chirality pdb=" C1 MAN I 5 " pdb=" O3 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 -2.61 5.01 2.00e-02 2.50e+03 6.28e+04 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 1.45 -3.85 2.00e-02 2.50e+03 3.70e+04 ... (remaining 2534 not shown) Planarity restraints: 2710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " -0.225 2.00e-02 2.50e+03 2.63e-01 8.63e+02 pdb=" CG ASN B 149 " 0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.423 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " -0.145 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" CG ASN C 149 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " 0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 80 " 0.078 2.00e-02 2.50e+03 7.96e-02 7.91e+01 pdb=" CG ASN B 80 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 80 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 80 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.096 2.00e-02 2.50e+03 ... (remaining 2707 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 133 2.58 - 3.16: 13309 3.16 - 3.74: 24311 3.74 - 4.32: 34308 4.32 - 4.90: 58212 Nonbonded interactions: 130273 Sorted by model distance: nonbonded pdb=" O PHE B 221 " pdb=" OG1 THR B 225 " model vdw 2.001 3.040 nonbonded pdb=" O PHE E 221 " pdb=" OG1 THR E 225 " model vdw 2.023 3.040 nonbonded pdb=" OD2 ASP L 8 " pdb=" O3 MAN J 4 " model vdw 2.086 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG SER F 408 " model vdw 2.091 3.040 nonbonded pdb=" OG SER B 51 " pdb=" OD1 ASP B 56 " model vdw 2.091 3.040 ... (remaining 130268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 416) selection = (chain 'D' and resid 12 through 416) } ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'E' and resid 8 through 447) } ncs_group { reference = (chain 'G' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) } ncs_group { reference = (chain 'K' and resid 1 through 67) selection = chain 'L' } 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.640 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16146 Z= 0.289 Angle : 0.744 10.328 21949 Z= 0.372 Chirality : 0.228 5.212 2537 Planarity : 0.004 0.075 2704 Dihedral : 15.410 128.741 6154 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.52 (0.20), residues: 1887 helix: 2.06 (0.21), residues: 593 sheet: -1.78 (0.22), residues: 500 loop : -1.16 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 237 HIS 0.004 0.001 HIS E 267 PHE 0.023 0.002 PHE A 258 TYR 0.027 0.002 TYR B 299 ARG 0.010 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 461 ASN cc_start: 0.7552 (m-40) cc_final: 0.7230 (m-40) REVERT: F 467 TYR cc_start: 0.6638 (m-80) cc_final: 0.6006 (m-80) REVERT: F 468 LEU cc_start: 0.7590 (tp) cc_final: 0.7111 (tp) REVERT: A 63 ASP cc_start: 0.7696 (m-30) cc_final: 0.7441 (m-30) REVERT: A 192 ASP cc_start: 0.7859 (t70) cc_final: 0.7615 (t0) REVERT: A 229 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8377 (mm-40) REVERT: A 274 ARG cc_start: 0.7725 (ttt-90) cc_final: 0.6842 (ttt180) REVERT: B 13 LYS cc_start: 0.9358 (tttm) cc_final: 0.9115 (tptm) REVERT: E 112 LYS cc_start: 0.8772 (tmmt) cc_final: 0.8538 (ttpt) REVERT: E 215 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8056 (tmtt) REVERT: E 224 GLN cc_start: 0.7852 (mp10) cc_final: 0.7570 (mt0) REVERT: E 227 MET cc_start: 0.7838 (mmt) cc_final: 0.7623 (mmt) REVERT: K 18 HIS cc_start: 0.6907 (m90) cc_final: 0.6622 (m-70) REVERT: L 5 ILE cc_start: 0.7383 (mm) cc_final: 0.7085 (mt) REVERT: L 32 ILE cc_start: 0.8053 (tt) cc_final: 0.7761 (pt) outliers start: 0 outliers final: 2 residues processed: 215 average time/residue: 1.4320 time to fit residues: 338.6324 Evaluate side-chains 148 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain B residue 172 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 189 ASN A 275 ASN B 113 ASN ** L 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 16146 Z= 0.314 Angle : 0.689 9.269 21949 Z= 0.340 Chirality : 0.046 0.280 2537 Planarity : 0.004 0.045 2704 Dihedral : 11.668 119.636 2603 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.59 % Allowed : 8.74 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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 (0.20), residues: 1887 helix: 2.19 (0.20), residues: 600 sheet: -1.48 (0.23), residues: 485 loop : -1.32 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 25 HIS 0.004 0.001 HIS E 119 PHE 0.018 0.002 PHE E 221 TYR 0.021 0.002 TYR E 299 ARG 0.005 0.000 ARG L 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.862 Fit side-chains REVERT: F 440 TRP cc_start: 0.7437 (m100) cc_final: 0.6879 (m100) REVERT: F 461 ASN cc_start: 0.7633 (m-40) cc_final: 0.7315 (m-40) REVERT: F 467 TYR cc_start: 0.6708 (m-80) cc_final: 0.6312 (m-80) REVERT: A 192 ASP cc_start: 0.7912 (t70) cc_final: 0.7636 (OUTLIER) REVERT: A 213 MET cc_start: 0.8416 (mmm) cc_final: 0.7525 (mmm) REVERT: A 229 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8344 (mm-40) REVERT: C 61 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8621 (ptt) REVERT: C 165 GLU cc_start: 0.7586 (tt0) cc_final: 0.7331 (mt-10) REVERT: E 148 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7603 (mm-40) REVERT: E 153 GLU cc_start: 0.8428 (tp30) cc_final: 0.8167 (tp30) REVERT: E 215 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8097 (tmtt) REVERT: K 18 HIS cc_start: 0.6982 (m90) cc_final: 0.6626 (m-70) REVERT: L 13 ASP cc_start: 0.5326 (OUTLIER) cc_final: 0.5063 (m-30) outliers start: 27 outliers final: 8 residues processed: 190 average time/residue: 1.3942 time to fit residues: 292.4710 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 113 ASN E 113 ASN D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16146 Z= 0.235 Angle : 0.632 10.353 21949 Z= 0.313 Chirality : 0.045 0.313 2537 Planarity : 0.004 0.041 2704 Dihedral : 10.310 115.625 2598 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.07 % Allowed : 11.58 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 1.22 % 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: -0.23 (0.20), residues: 1887 helix: 2.27 (0.20), residues: 605 sheet: -1.34 (0.23), residues: 482 loop : -1.27 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 25 HIS 0.003 0.001 HIS E 267 PHE 0.019 0.001 PHE E 221 TYR 0.024 0.001 TYR E 277 ARG 0.003 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 461 ASN cc_start: 0.7603 (m-40) cc_final: 0.7382 (m-40) REVERT: F 474 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8723 (mmtt) REVERT: A 192 ASP cc_start: 0.7890 (t70) cc_final: 0.7629 (t0) REVERT: A 229 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8378 (mm-40) REVERT: A 274 ARG cc_start: 0.7788 (ttt-90) cc_final: 0.7506 (ttt90) REVERT: C 61 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8497 (ptt) REVERT: C 153 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: C 283 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: E 215 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8079 (tmtt) REVERT: E 429 ILE cc_start: 0.8559 (mp) cc_final: 0.8345 (mt) REVERT: D 58 MET cc_start: 0.8035 (tpt) cc_final: 0.7777 (tpt) REVERT: K 18 HIS cc_start: 0.6854 (m90) cc_final: 0.6546 (m-70) outliers start: 35 outliers final: 15 residues processed: 176 average time/residue: 1.2799 time to fit residues: 250.8817 Evaluate side-chains 168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN F 504 GLN C 85 ASN E 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16146 Z= 0.185 Angle : 0.607 8.711 21949 Z= 0.299 Chirality : 0.044 0.286 2537 Planarity : 0.003 0.038 2704 Dihedral : 9.619 113.254 2598 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.36 % Allowed : 12.64 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.06 (0.20), residues: 1887 helix: 2.35 (0.20), residues: 605 sheet: -1.30 (0.23), residues: 479 loop : -1.08 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 25 HIS 0.004 0.001 HIS E 267 PHE 0.017 0.001 PHE E 221 TYR 0.023 0.001 TYR E 299 ARG 0.002 0.000 ARG F 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 474 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8741 (mmtt) REVERT: A 192 ASP cc_start: 0.7886 (t70) cc_final: 0.7610 (t0) REVERT: A 213 MET cc_start: 0.8429 (mmm) cc_final: 0.7419 (mmm) REVERT: A 229 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8348 (mm-40) REVERT: A 274 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7642 (ttt-90) REVERT: B 49 MET cc_start: 0.7863 (ptt) cc_final: 0.7631 (pp-130) REVERT: B 61 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8247 (ptt) REVERT: B 224 GLN cc_start: 0.7336 (mp10) cc_final: 0.6633 (mm110) REVERT: C 153 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: C 185 GLN cc_start: 0.8585 (pm20) cc_final: 0.8360 (pm20) REVERT: E 153 GLU cc_start: 0.8348 (tp30) cc_final: 0.8133 (tp30) REVERT: E 215 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8071 (tmtt) REVERT: E 429 ILE cc_start: 0.8526 (mp) cc_final: 0.8326 (mt) REVERT: D 15 PHE cc_start: 0.8061 (m-80) cc_final: 0.7670 (t80) REVERT: K 18 HIS cc_start: 0.6929 (m90) cc_final: 0.6586 (m-70) outliers start: 40 outliers final: 12 residues processed: 188 average time/residue: 1.2164 time to fit residues: 256.2799 Evaluate side-chains 164 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 16146 Z= 0.361 Angle : 0.666 9.471 21949 Z= 0.331 Chirality : 0.046 0.261 2537 Planarity : 0.004 0.037 2704 Dihedral : 9.554 111.534 2598 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.24 % Allowed : 14.18 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.06 (0.20), residues: 1887 helix: 2.29 (0.20), residues: 605 sheet: -1.30 (0.22), residues: 509 loop : -0.98 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 25 HIS 0.004 0.001 HIS E 119 PHE 0.022 0.002 PHE D 304 TYR 0.023 0.002 TYR E 299 ARG 0.004 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7889 (t70) cc_final: 0.7627 (t0) REVERT: A 229 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8396 (mm-40) REVERT: A 274 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7716 (ttt-90) REVERT: B 49 MET cc_start: 0.7900 (ptt) cc_final: 0.7625 (pp-130) REVERT: C 153 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: C 185 GLN cc_start: 0.8610 (pm20) cc_final: 0.8403 (pm20) REVERT: E 147 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8802 (tm-30) REVERT: E 148 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7613 (mm-40) REVERT: E 215 LYS cc_start: 0.8547 (tmtt) cc_final: 0.8127 (tmtt) REVERT: E 429 ILE cc_start: 0.8612 (mp) cc_final: 0.8353 (mt) REVERT: D 15 PHE cc_start: 0.8204 (m-80) cc_final: 0.7938 (t80) REVERT: D 58 MET cc_start: 0.8132 (tpt) cc_final: 0.7930 (tpt) REVERT: K 18 HIS cc_start: 0.6748 (m90) cc_final: 0.6460 (m-70) outliers start: 38 outliers final: 16 residues processed: 180 average time/residue: 1.2822 time to fit residues: 256.9219 Evaluate side-chains 159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 151 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 96 optimal weight: 0.0770 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16146 Z= 0.186 Angle : 0.625 10.089 21949 Z= 0.308 Chirality : 0.044 0.282 2537 Planarity : 0.003 0.038 2704 Dihedral : 9.149 110.666 2598 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.65 % Allowed : 15.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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 (0.20), residues: 1887 helix: 2.35 (0.20), residues: 605 sheet: -1.15 (0.23), residues: 488 loop : -0.94 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 25 HIS 0.005 0.001 HIS E 267 PHE 0.015 0.001 PHE F 455 TYR 0.023 0.001 TYR E 299 ARG 0.002 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7888 (t70) cc_final: 0.7610 (t0) REVERT: A 213 MET cc_start: 0.8498 (mmm) cc_final: 0.7329 (mmm) REVERT: A 229 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8411 (mm-40) REVERT: B 49 MET cc_start: 0.7877 (ptt) cc_final: 0.7632 (pp-130) REVERT: C 153 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: C 223 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7430 (tm) REVERT: E 148 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7525 (mm-40) REVERT: E 429 ILE cc_start: 0.8503 (mp) cc_final: 0.8289 (mt) REVERT: D 15 PHE cc_start: 0.8161 (m-80) cc_final: 0.7923 (t80) REVERT: K 18 HIS cc_start: 0.6779 (m90) cc_final: 0.6449 (m-70) outliers start: 28 outliers final: 18 residues processed: 169 average time/residue: 1.1990 time to fit residues: 227.2164 Evaluate side-chains 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 116 ASN D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 16146 Z= 0.362 Angle : 0.690 10.156 21949 Z= 0.340 Chirality : 0.046 0.248 2537 Planarity : 0.004 0.039 2704 Dihedral : 9.133 108.411 2598 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.01 % Allowed : 15.48 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.01 (0.20), residues: 1887 helix: 2.10 (0.20), residues: 623 sheet: -1.20 (0.22), residues: 501 loop : -0.87 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 440 HIS 0.004 0.001 HIS A 110 PHE 0.021 0.002 PHE D 304 TYR 0.023 0.002 TYR E 299 ARG 0.003 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 440 TRP cc_start: 0.7613 (m100) cc_final: 0.7245 (m100) REVERT: F 452 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8762 (tptp) REVERT: A 192 ASP cc_start: 0.7885 (t70) cc_final: 0.7624 (t0) REVERT: A 229 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8431 (mm-40) REVERT: B 49 MET cc_start: 0.7881 (ptt) cc_final: 0.7615 (pp-130) REVERT: C 153 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: C 223 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7596 (tm) REVERT: C 286 MET cc_start: 0.8227 (tpp) cc_final: 0.7699 (tpp) REVERT: E 153 GLU cc_start: 0.8374 (tp30) cc_final: 0.8085 (tp30) REVERT: E 215 LYS cc_start: 0.8547 (tmtt) cc_final: 0.8120 (tmtt) REVERT: D 15 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (t80) REVERT: D 58 MET cc_start: 0.8237 (tpt) cc_final: 0.7966 (tpt) REVERT: K 18 HIS cc_start: 0.6744 (m90) cc_final: 0.6456 (m-70) REVERT: L 13 ASP cc_start: 0.6658 (m-30) cc_final: 0.6311 (m-30) outliers start: 34 outliers final: 18 residues processed: 167 average time/residue: 1.2884 time to fit residues: 239.9316 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN D 242 GLN D 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16146 Z= 0.183 Angle : 0.644 12.175 21949 Z= 0.315 Chirality : 0.044 0.277 2537 Planarity : 0.004 0.038 2704 Dihedral : 8.755 107.718 2598 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 15.89 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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 (0.20), residues: 1887 helix: 2.24 (0.20), residues: 617 sheet: -1.06 (0.23), residues: 492 loop : -0.85 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 440 HIS 0.005 0.001 HIS E 267 PHE 0.011 0.001 PHE A 404 TYR 0.023 0.001 TYR E 299 ARG 0.002 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: F 452 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8761 (tptp) REVERT: F 474 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8835 (mmtt) REVERT: F 501 TYR cc_start: 0.8180 (m-80) cc_final: 0.7928 (m-80) REVERT: A 192 ASP cc_start: 0.7883 (t70) cc_final: 0.7611 (t0) REVERT: A 213 MET cc_start: 0.8490 (mmm) cc_final: 0.7332 (mmm) REVERT: A 229 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8413 (mm-40) REVERT: B 49 MET cc_start: 0.7882 (ptt) cc_final: 0.7617 (pp-130) REVERT: B 61 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8236 (ptt) REVERT: C 153 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: C 223 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7525 (tm) REVERT: C 286 MET cc_start: 0.8103 (tpp) cc_final: 0.7562 (tpp) REVERT: E 153 GLU cc_start: 0.8282 (tp30) cc_final: 0.7869 (tp30) REVERT: E 207 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8091 (tpt-90) REVERT: E 215 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8062 (tmtt) REVERT: E 429 ILE cc_start: 0.8418 (mp) cc_final: 0.8201 (mt) REVERT: D 15 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7953 (t80) REVERT: K 18 HIS cc_start: 0.6829 (m90) cc_final: 0.6479 (m-70) REVERT: L 13 ASP cc_start: 0.6515 (m-30) cc_final: 0.6151 (m-30) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 1.2097 time to fit residues: 225.1427 Evaluate side-chains 162 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 0.0570 chunk 160 optimal weight: 6.9990 chunk 111 optimal weight: 0.0040 chunk 179 optimal weight: 0.4980 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 303 ASN D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16146 Z= 0.168 Angle : 0.647 11.318 21949 Z= 0.313 Chirality : 0.044 0.260 2537 Planarity : 0.003 0.037 2704 Dihedral : 8.472 105.239 2598 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.48 % Allowed : 16.66 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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 (0.20), residues: 1887 helix: 2.46 (0.20), residues: 605 sheet: -0.86 (0.23), residues: 482 loop : -0.93 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 440 HIS 0.005 0.001 HIS E 267 PHE 0.011 0.001 PHE A 404 TYR 0.024 0.001 TYR E 299 ARG 0.004 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 451 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8619 (m) REVERT: F 452 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8810 (tptp) REVERT: F 501 TYR cc_start: 0.8201 (m-80) cc_final: 0.7955 (m-80) REVERT: A 192 ASP cc_start: 0.7876 (t70) cc_final: 0.7590 (t0) REVERT: A 213 MET cc_start: 0.8408 (mmm) cc_final: 0.7338 (mmm) REVERT: A 229 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8320 (mm-40) REVERT: B 49 MET cc_start: 0.7893 (ptt) cc_final: 0.7677 (pp-130) REVERT: C 223 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7260 (tm) REVERT: C 286 MET cc_start: 0.8051 (tpp) cc_final: 0.7578 (tpp) REVERT: E 429 ILE cc_start: 0.8394 (mp) cc_final: 0.8191 (mt) REVERT: D 15 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7933 (t80) REVERT: K 18 HIS cc_start: 0.6451 (m90) cc_final: 0.6132 (m-70) REVERT: L 13 ASP cc_start: 0.6348 (m-30) cc_final: 0.6064 (m-30) outliers start: 25 outliers final: 15 residues processed: 160 average time/residue: 1.1617 time to fit residues: 209.1845 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 0.0370 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 116 ASN D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16146 Z= 0.182 Angle : 0.659 12.389 21949 Z= 0.316 Chirality : 0.044 0.250 2537 Planarity : 0.003 0.039 2704 Dihedral : 8.328 103.336 2598 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.42 % Allowed : 16.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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 (0.20), residues: 1887 helix: 2.48 (0.20), residues: 605 sheet: -0.82 (0.23), residues: 485 loop : -0.88 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP F 440 HIS 0.005 0.001 HIS E 267 PHE 0.020 0.001 PHE C 433 TYR 0.031 0.001 TYR E 277 ARG 0.003 0.000 ARG A 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: F 451 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8590 (m) REVERT: F 452 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8831 (tptp) REVERT: F 501 TYR cc_start: 0.8235 (m-80) cc_final: 0.7966 (m-80) REVERT: A 192 ASP cc_start: 0.7878 (t70) cc_final: 0.7602 (t0) REVERT: A 213 MET cc_start: 0.8412 (mmm) cc_final: 0.7405 (mmm) REVERT: A 229 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8296 (mm-40) REVERT: B 49 MET cc_start: 0.7906 (ptt) cc_final: 0.7685 (pp-130) REVERT: C 286 MET cc_start: 0.8068 (tpp) cc_final: 0.7580 (tpp) REVERT: E 429 ILE cc_start: 0.8397 (mp) cc_final: 0.8192 (mt) REVERT: D 15 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (t80) REVERT: D 131 MET cc_start: 0.8895 (ptm) cc_final: 0.8649 (ptm) REVERT: K 18 HIS cc_start: 0.6724 (m90) cc_final: 0.6377 (m-70) REVERT: L 13 ASP cc_start: 0.6419 (m-30) cc_final: 0.6057 (m-30) outliers start: 24 outliers final: 16 residues processed: 166 average time/residue: 1.1696 time to fit residues: 218.9732 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.081922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062299 restraints weight = 41184.528| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.34 r_work: 0.2935 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16146 Z= 0.234 Angle : 0.678 13.813 21949 Z= 0.326 Chirality : 0.045 0.267 2537 Planarity : 0.004 0.039 2704 Dihedral : 8.290 102.373 2598 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.24 % Allowed : 17.25 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 0.33 (0.20), residues: 1887 helix: 2.49 (0.20), residues: 605 sheet: -0.83 (0.23), residues: 505 loop : -0.84 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 440 HIS 0.005 0.001 HIS E 267 PHE 0.018 0.001 PHE C 433 TYR 0.024 0.001 TYR E 299 ARG 0.004 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.61 seconds wall clock time: 90 minutes 37.70 seconds (5437.70 seconds total)