Starting phenix.real_space_refine on Wed Mar 4 22:02:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_13315.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_13315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_13315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_13315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pc0_13315/03_2026/7pc0_13315.map" } resolution = 3.0 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 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.60, per 1000 atoms: 0.23 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: 1.31 Conformation dependent library (CDL) restraints added in 768.2 milliseconds 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: 0.43 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: 2.19 Time building geometry restraints manager: 1.68 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 : 0.005 0.243 16191 Z= 0.211 Angle : 1.238 58.623 22054 Z= 0.502 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.000 ARG E 114 TYR 0.027 0.002 TYR B 299 PHE 0.023 0.002 PHE A 258 TRP 0.014 0.001 TRP B 237 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00434 (16146) covalent geometry : angle 0.74386 (21949) SS BOND : bond 0.00985 ( 21) SS BOND : angle 4.60341 ( 42) hydrogen bonds : bond 0.11060 ( 637) hydrogen bonds : angle 5.52438 ( 1797) metal coordination : bond 0.15208 ( 3) link_ALPHA1-3 : bond 0.00773 ( 4) link_ALPHA1-3 : angle 16.90074 ( 12) link_ALPHA1-6 : bond 0.01040 ( 4) link_ALPHA1-6 : angle 24.42084 ( 12) link_BETA1-4 : bond 0.01607 ( 7) link_BETA1-4 : angle 16.63797 ( 21) link_NAG-ASN : bond 0.04570 ( 6) link_NAG-ASN : angle 15.57462 ( 18) *********************** 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 : 0.611 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: 0.6371 time to fit residues: 150.3138 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 : 0.547 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.080158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060295 restraints weight = 41282.024| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.31 r_work: 0.2887 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.147 16191 Z= 0.291 Angle : 0.778 11.313 22054 Z= 0.381 Chirality : 0.048 0.257 2537 Planarity : 0.005 0.046 2704 Dihedral : 11.697 119.036 2603 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.77 % Allowed : 9.27 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1887 helix: 2.00 (0.20), residues: 613 sheet: -1.65 (0.22), residues: 500 loop : -1.30 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 28 TYR 0.020 0.002 TYR E 299 PHE 0.022 0.002 PHE D 304 TRP 0.018 0.001 TRP L 25 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00678 (16146) covalent geometry : angle 0.74614 (21949) SS BOND : bond 0.00698 ( 21) SS BOND : angle 3.66566 ( 42) hydrogen bonds : bond 0.04689 ( 637) hydrogen bonds : angle 5.04052 ( 1797) metal coordination : bond 0.00794 ( 3) link_ALPHA1-3 : bond 0.01110 ( 4) link_ALPHA1-3 : angle 3.73971 ( 12) link_ALPHA1-6 : bond 0.01465 ( 4) link_ALPHA1-6 : angle 3.12768 ( 12) link_BETA1-4 : bond 0.00586 ( 7) link_BETA1-4 : angle 2.53545 ( 21) link_NAG-ASN : bond 0.00447 ( 6) link_NAG-ASN : angle 2.96112 ( 18) *********************** 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 194 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 461 ASN cc_start: 0.8021 (m-40) cc_final: 0.7769 (m-40) REVERT: F 467 TYR cc_start: 0.6983 (m-80) cc_final: 0.6609 (m-80) REVERT: A 192 ASP cc_start: 0.8430 (t70) cc_final: 0.8082 (t0) REVERT: A 213 MET cc_start: 0.8913 (mmm) cc_final: 0.7996 (mmm) REVERT: A 229 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8479 (mm-40) REVERT: C 49 MET cc_start: 0.7745 (tmm) cc_final: 0.7469 (tmm) REVERT: C 61 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9111 (ptt) REVERT: C 227 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7957 (ttp) REVERT: E 14 GLU cc_start: 0.8848 (pp20) cc_final: 0.8589 (pp20) REVERT: E 148 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7773 (mm-40) REVERT: E 153 GLU cc_start: 0.8950 (tp30) cc_final: 0.8672 (tp30) REVERT: E 180 ARG cc_start: 0.8575 (mpt180) cc_final: 0.8372 (mpp-170) REVERT: E 215 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8055 (tmtt) REVERT: K 18 HIS cc_start: 0.7572 (m90) cc_final: 0.7145 (m-70) REVERT: L 32 ILE cc_start: 0.7792 (tt) cc_final: 0.7548 (pt) outliers start: 30 outliers final: 9 residues processed: 181 average time/residue: 0.6225 time to fit residues: 124.2730 Evaluate side-chains 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER 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 227 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 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.081918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062132 restraints weight = 41616.936| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.36 r_work: 0.2931 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16191 Z= 0.147 Angle : 0.650 9.868 22054 Z= 0.318 Chirality : 0.045 0.305 2537 Planarity : 0.004 0.042 2704 Dihedral : 10.309 115.393 2598 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.01 % Allowed : 12.11 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1887 helix: 2.24 (0.20), residues: 606 sheet: -1.41 (0.23), residues: 483 loop : -1.28 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.023 0.001 TYR E 299 PHE 0.018 0.001 PHE E 221 TRP 0.016 0.001 TRP L 25 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00335 (16146) covalent geometry : angle 0.62595 (21949) SS BOND : bond 0.00508 ( 21) SS BOND : angle 3.02378 ( 42) hydrogen bonds : bond 0.03920 ( 637) hydrogen bonds : angle 4.79647 ( 1797) metal coordination : bond 0.00498 ( 3) link_ALPHA1-3 : bond 0.01277 ( 4) link_ALPHA1-3 : angle 3.32034 ( 12) link_ALPHA1-6 : bond 0.01596 ( 4) link_ALPHA1-6 : angle 2.26967 ( 12) link_BETA1-4 : bond 0.00593 ( 7) link_BETA1-4 : angle 1.60435 ( 21) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.21536 ( 18) *********************** 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 193 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: F 440 TRP cc_start: 0.7171 (m100) cc_final: 0.6926 (m100) REVERT: F 461 ASN cc_start: 0.7991 (m-40) cc_final: 0.7702 (m-40) REVERT: F 472 ASN cc_start: 0.8820 (m110) cc_final: 0.8443 (p0) REVERT: F 474 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8597 (mmtt) REVERT: A 192 ASP cc_start: 0.8420 (t70) cc_final: 0.8067 (t0) REVERT: A 229 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8513 (mm-40) REVERT: A 236 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7869 (mtm) REVERT: B 49 MET cc_start: 0.8563 (ptt) cc_final: 0.7948 (pp-130) REVERT: B 84 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8446 (t0) REVERT: C 49 MET cc_start: 0.7803 (tmm) cc_final: 0.7282 (tmm) REVERT: C 61 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9012 (ptt) REVERT: C 283 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7445 (mpp) REVERT: E 147 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8770 (tm-30) REVERT: E 215 LYS cc_start: 0.8524 (tmtt) cc_final: 0.8061 (tmtt) REVERT: K 18 HIS cc_start: 0.7394 (m90) cc_final: 0.7049 (m-70) REVERT: L 10 THR cc_start: 0.8510 (t) cc_final: 0.8300 (t) REVERT: L 32 ILE cc_start: 0.7883 (tt) cc_final: 0.7639 (pt) outliers start: 34 outliers final: 13 residues processed: 178 average time/residue: 0.5820 time to fit residues: 115.0446 Evaluate side-chains 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 236 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 84 ASP 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 283 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 79 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN B 224 GLN C 85 ASN D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061339 restraints weight = 41423.901| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.34 r_work: 0.2911 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 16191 Z= 0.174 Angle : 0.648 10.169 22054 Z= 0.317 Chirality : 0.045 0.280 2537 Planarity : 0.004 0.038 2704 Dihedral : 9.777 112.776 2598 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.60 % Allowed : 12.70 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1887 helix: 2.17 (0.20), residues: 619 sheet: -1.34 (0.22), residues: 494 loop : -1.03 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 33 TYR 0.023 0.001 TYR E 299 PHE 0.018 0.001 PHE E 221 TRP 0.014 0.001 TRP L 25 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00406 (16146) covalent geometry : angle 0.62672 (21949) SS BOND : bond 0.00427 ( 21) SS BOND : angle 2.82727 ( 42) hydrogen bonds : bond 0.03929 ( 637) hydrogen bonds : angle 4.74803 ( 1797) metal coordination : bond 0.00107 ( 3) link_ALPHA1-3 : bond 0.01200 ( 4) link_ALPHA1-3 : angle 3.26208 ( 12) link_ALPHA1-6 : bond 0.01375 ( 4) link_ALPHA1-6 : angle 2.10001 ( 12) link_BETA1-4 : bond 0.00484 ( 7) link_BETA1-4 : angle 1.57041 ( 21) link_NAG-ASN : bond 0.00170 ( 6) link_NAG-ASN : angle 1.99227 ( 18) *********************** 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 205 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: F 474 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8740 (mmtt) REVERT: A 192 ASP cc_start: 0.8418 (t70) cc_final: 0.8072 (t0) REVERT: A 229 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8542 (mm-40) REVERT: A 274 ARG cc_start: 0.7861 (ttt90) cc_final: 0.7529 (ttt-90) REVERT: B 49 MET cc_start: 0.8559 (ptt) cc_final: 0.7941 (pp-130) REVERT: B 61 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.8639 (ptt) REVERT: B 84 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8432 (t0) REVERT: B 115 MET cc_start: 0.8880 (ptt) cc_final: 0.8592 (ptm) REVERT: C 49 MET cc_start: 0.7841 (tmm) cc_final: 0.7389 (tmm) REVERT: C 61 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9008 (ptt) REVERT: C 185 GLN cc_start: 0.8722 (pm20) cc_final: 0.8335 (pm20) REVERT: E 179 GLU cc_start: 0.8875 (mp0) cc_final: 0.8627 (mp0) REVERT: E 180 ARG cc_start: 0.8398 (mpt180) cc_final: 0.8117 (mpp-170) REVERT: E 215 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8060 (tmtt) REVERT: E 429 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8275 (mt) REVERT: K 18 HIS cc_start: 0.7406 (m90) cc_final: 0.6993 (m-70) REVERT: L 32 ILE cc_start: 0.7929 (tt) cc_final: 0.7680 (pt) outliers start: 44 outliers final: 14 residues processed: 187 average time/residue: 0.5372 time to fit residues: 111.7885 Evaluate side-chains 163 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 84 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 111 VAL 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 E residue 429 ILE 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 L residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 113 optimal weight: 0.0050 chunk 186 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0270 chunk 40 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.081946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062203 restraints weight = 41251.353| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.34 r_work: 0.2930 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16191 Z= 0.134 Angle : 0.632 10.928 22054 Z= 0.308 Chirality : 0.044 0.290 2537 Planarity : 0.003 0.037 2704 Dihedral : 9.434 112.060 2598 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.07 % Allowed : 14.00 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1887 helix: 2.34 (0.20), residues: 606 sheet: -1.25 (0.23), residues: 499 loop : -0.99 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 432 TYR 0.023 0.001 TYR E 299 PHE 0.014 0.001 PHE D 304 TRP 0.013 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00306 (16146) covalent geometry : angle 0.61136 (21949) SS BOND : bond 0.00411 ( 21) SS BOND : angle 2.79241 ( 42) hydrogen bonds : bond 0.03644 ( 637) hydrogen bonds : angle 4.64205 ( 1797) metal coordination : bond 0.00340 ( 3) link_ALPHA1-3 : bond 0.01160 ( 4) link_ALPHA1-3 : angle 3.30577 ( 12) link_ALPHA1-6 : bond 0.01376 ( 4) link_ALPHA1-6 : angle 1.97779 ( 12) link_BETA1-4 : bond 0.00526 ( 7) link_BETA1-4 : angle 1.49144 ( 21) link_NAG-ASN : bond 0.00194 ( 6) link_NAG-ASN : angle 1.84626 ( 18) *********************** 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 190 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 440 TRP cc_start: 0.7404 (m100) cc_final: 0.6990 (m100) REVERT: A 192 ASP cc_start: 0.8415 (t70) cc_final: 0.8054 (t0) REVERT: A 213 MET cc_start: 0.8939 (mmm) cc_final: 0.7759 (mmm) REVERT: A 229 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8477 (mm-40) REVERT: A 274 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7695 (ttt-90) REVERT: B 49 MET cc_start: 0.8563 (ptt) cc_final: 0.7954 (pp-130) REVERT: B 61 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8552 (ptt) REVERT: B 84 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8425 (t0) REVERT: C 49 MET cc_start: 0.7832 (tmm) cc_final: 0.7369 (tmm) REVERT: C 185 GLN cc_start: 0.8728 (pm20) cc_final: 0.8414 (pm20) REVERT: E 153 GLU cc_start: 0.8920 (tp30) cc_final: 0.8649 (tp30) REVERT: E 180 ARG cc_start: 0.8319 (mpt180) cc_final: 0.8114 (mpp-170) REVERT: E 215 LYS cc_start: 0.8549 (tmtt) cc_final: 0.8115 (tmtt) REVERT: E 429 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (mt) REVERT: K 18 HIS cc_start: 0.7275 (m90) cc_final: 0.6916 (m-70) REVERT: L 32 ILE cc_start: 0.8008 (tt) cc_final: 0.7756 (pt) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 0.5713 time to fit residues: 112.2100 Evaluate side-chains 162 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL 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 84 ASP 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 E residue 115 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 429 ILE 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 K residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 167 optimal weight: 0.4980 chunk 18 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 chunk 96 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN E 185 GLN D 242 GLN D 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063215 restraints weight = 40945.740| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.35 r_work: 0.2959 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16191 Z= 0.112 Angle : 0.633 10.763 22054 Z= 0.304 Chirality : 0.044 0.282 2537 Planarity : 0.003 0.036 2704 Dihedral : 9.047 110.535 2598 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.54 % Allowed : 15.24 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1887 helix: 2.44 (0.20), residues: 605 sheet: -1.09 (0.23), residues: 485 loop : -0.94 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.023 0.001 TYR E 299 PHE 0.013 0.001 PHE C 433 TRP 0.011 0.001 TRP L 25 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00247 (16146) covalent geometry : angle 0.61314 (21949) SS BOND : bond 0.00414 ( 21) SS BOND : angle 2.68259 ( 42) hydrogen bonds : bond 0.03349 ( 637) hydrogen bonds : angle 4.52837 ( 1797) metal coordination : bond 0.00548 ( 3) link_ALPHA1-3 : bond 0.01167 ( 4) link_ALPHA1-3 : angle 3.26832 ( 12) link_ALPHA1-6 : bond 0.01356 ( 4) link_ALPHA1-6 : angle 1.85492 ( 12) link_BETA1-4 : bond 0.00544 ( 7) link_BETA1-4 : angle 1.44857 ( 21) link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 1.75907 ( 18) *********************** 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 190 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 451 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8626 (m) REVERT: F 452 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8797 (tptp) REVERT: A 192 ASP cc_start: 0.8384 (t70) cc_final: 0.8017 (t0) REVERT: A 213 MET cc_start: 0.8860 (mmm) cc_final: 0.7829 (mmm) REVERT: A 229 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8469 (mm-40) REVERT: A 274 ARG cc_start: 0.8062 (ttt90) cc_final: 0.7634 (ttt-90) REVERT: B 49 MET cc_start: 0.8562 (ptt) cc_final: 0.7958 (pp-130) REVERT: B 61 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8074 (ptp) REVERT: B 84 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 115 MET cc_start: 0.8737 (ptt) cc_final: 0.8506 (ptm) REVERT: C 49 MET cc_start: 0.7784 (tmm) cc_final: 0.7581 (tmm) REVERT: C 185 GLN cc_start: 0.8691 (pm20) cc_final: 0.8430 (pm20) REVERT: C 286 MET cc_start: 0.8254 (tpp) cc_final: 0.8051 (tpp) REVERT: E 112 LYS cc_start: 0.9023 (tttm) cc_final: 0.8804 (tmmt) REVERT: E 153 GLU cc_start: 0.8895 (tp30) cc_final: 0.8625 (tp30) REVERT: E 180 ARG cc_start: 0.8286 (mpt180) cc_final: 0.8063 (mpp-170) REVERT: E 215 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8007 (tmtt) REVERT: E 429 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (mt) REVERT: K 18 HIS cc_start: 0.7365 (m90) cc_final: 0.6922 (m-70) REVERT: L 32 ILE cc_start: 0.8013 (tt) cc_final: 0.7766 (pt) outliers start: 26 outliers final: 13 residues processed: 181 average time/residue: 0.5467 time to fit residues: 110.4721 Evaluate side-chains 162 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL 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 84 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 429 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 13 optimal weight: 0.0870 chunk 97 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.061060 restraints weight = 41370.279| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.34 r_work: 0.2901 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 16191 Z= 0.200 Angle : 0.675 11.587 22054 Z= 0.328 Chirality : 0.045 0.251 2537 Planarity : 0.004 0.035 2704 Dihedral : 9.004 108.602 2598 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.42 % Allowed : 16.01 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1887 helix: 2.43 (0.20), residues: 606 sheet: -1.07 (0.23), residues: 494 loop : -0.92 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 33 TYR 0.023 0.001 TYR E 299 PHE 0.019 0.001 PHE D 304 TRP 0.017 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00470 (16146) covalent geometry : angle 0.65603 (21949) SS BOND : bond 0.00601 ( 21) SS BOND : angle 2.76684 ( 42) hydrogen bonds : bond 0.03905 ( 637) hydrogen bonds : angle 4.64623 ( 1797) metal coordination : bond 0.00122 ( 3) link_ALPHA1-3 : bond 0.01013 ( 4) link_ALPHA1-3 : angle 3.29021 ( 12) link_ALPHA1-6 : bond 0.01240 ( 4) link_ALPHA1-6 : angle 1.69295 ( 12) link_BETA1-4 : bond 0.00540 ( 7) link_BETA1-4 : angle 1.55521 ( 21) link_NAG-ASN : bond 0.00174 ( 6) link_NAG-ASN : angle 1.84241 ( 18) *********************** 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 168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8409 (t70) cc_final: 0.8060 (t0) REVERT: A 229 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8477 (mm-40) REVERT: B 49 MET cc_start: 0.8526 (ptt) cc_final: 0.7926 (pp-130) REVERT: B 61 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.8108 (ptp) REVERT: C 49 MET cc_start: 0.7832 (tmm) cc_final: 0.7565 (tmm) REVERT: C 137 MET cc_start: 0.9149 (mpp) cc_final: 0.8896 (mmp) REVERT: C 185 GLN cc_start: 0.8714 (pm20) cc_final: 0.8451 (pm20) REVERT: E 153 GLU cc_start: 0.8937 (tp30) cc_final: 0.8493 (tp30) REVERT: E 180 ARG cc_start: 0.8294 (mpt180) cc_final: 0.7989 (mpp-170) REVERT: E 207 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8218 (tpt-90) REVERT: D 15 PHE cc_start: 0.8286 (m-80) cc_final: 0.7856 (t80) REVERT: K 18 HIS cc_start: 0.7235 (m90) cc_final: 0.6874 (m-70) REVERT: L 32 ILE cc_start: 0.8063 (tt) cc_final: 0.7836 (pt) outliers start: 24 outliers final: 16 residues processed: 161 average time/residue: 0.5612 time to fit residues: 100.5037 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 : 0.601 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL 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 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 106 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 187 optimal weight: 40.0000 chunk 79 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062776 restraints weight = 41278.720| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.35 r_work: 0.2944 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16191 Z= 0.125 Angle : 0.664 11.756 22054 Z= 0.318 Chirality : 0.044 0.269 2537 Planarity : 0.003 0.036 2704 Dihedral : 8.712 107.784 2598 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.36 % Allowed : 16.60 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1887 helix: 2.46 (0.20), residues: 606 sheet: -0.97 (0.23), residues: 491 loop : -0.92 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.023 0.001 TYR E 299 PHE 0.011 0.001 PHE B 98 TRP 0.019 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00281 (16146) covalent geometry : angle 0.64653 (21949) SS BOND : bond 0.00403 ( 21) SS BOND : angle 2.62455 ( 42) hydrogen bonds : bond 0.03477 ( 637) hydrogen bonds : angle 4.52596 ( 1797) metal coordination : bond 0.00353 ( 3) link_ALPHA1-3 : bond 0.01114 ( 4) link_ALPHA1-3 : angle 3.25398 ( 12) link_ALPHA1-6 : bond 0.01355 ( 4) link_ALPHA1-6 : angle 1.74439 ( 12) link_BETA1-4 : bond 0.00593 ( 7) link_BETA1-4 : angle 1.44055 ( 21) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.68337 ( 18) *********************** 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 175 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8415 (t70) cc_final: 0.8056 (t0) REVERT: A 213 MET cc_start: 0.8912 (mmm) cc_final: 0.7954 (mmm) REVERT: A 229 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8430 (mm-40) REVERT: A 274 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.7782 (mtp85) REVERT: B 49 MET cc_start: 0.8565 (ptt) cc_final: 0.7981 (pp-130) REVERT: B 61 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8114 (ptp) REVERT: B 84 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8625 (t0) REVERT: C 137 MET cc_start: 0.9151 (mpp) cc_final: 0.8906 (mmp) REVERT: C 185 GLN cc_start: 0.8709 (pm20) cc_final: 0.8443 (pm20) REVERT: E 153 GLU cc_start: 0.8907 (tp30) cc_final: 0.8443 (tp30) REVERT: E 207 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8306 (tpt-90) REVERT: E 429 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8178 (mt) REVERT: D 15 PHE cc_start: 0.8283 (m-80) cc_final: 0.7843 (t80) REVERT: D 229 GLN cc_start: 0.8914 (tp40) cc_final: 0.8646 (tp40) REVERT: K 18 HIS cc_start: 0.7370 (m90) cc_final: 0.6917 (m-70) REVERT: L 32 ILE cc_start: 0.8120 (tt) cc_final: 0.7885 (pt) outliers start: 23 outliers final: 15 residues processed: 168 average time/residue: 0.5325 time to fit residues: 100.0252 Evaluate side-chains 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL 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 84 ASP 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 E residue 238 VAL Chi-restraints excluded: chain E residue 429 ILE 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 48 optimal weight: 0.0470 chunk 129 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 125 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063332 restraints weight = 41259.248| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.36 r_work: 0.2960 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16191 Z= 0.117 Angle : 0.665 11.497 22054 Z= 0.317 Chirality : 0.044 0.253 2537 Planarity : 0.003 0.036 2704 Dihedral : 8.461 105.079 2598 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.12 % Allowed : 16.89 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1887 helix: 2.47 (0.20), residues: 606 sheet: -0.83 (0.24), residues: 484 loop : -0.91 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.028 0.001 TYR E 277 PHE 0.019 0.001 PHE C 433 TRP 0.022 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00264 (16146) covalent geometry : angle 0.64724 (21949) SS BOND : bond 0.00435 ( 21) SS BOND : angle 2.66988 ( 42) hydrogen bonds : bond 0.03375 ( 637) hydrogen bonds : angle 4.47661 ( 1797) metal coordination : bond 0.00383 ( 3) link_ALPHA1-3 : bond 0.01113 ( 4) link_ALPHA1-3 : angle 3.27554 ( 12) link_ALPHA1-6 : bond 0.01241 ( 4) link_ALPHA1-6 : angle 1.63966 ( 12) link_BETA1-4 : bond 0.00565 ( 7) link_BETA1-4 : angle 1.43173 ( 21) link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 1.63506 ( 18) *********************** 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: 19 poor density : 150 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 451 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8638 (m) REVERT: F 501 TYR cc_start: 0.8175 (m-80) cc_final: 0.7860 (m-80) REVERT: A 112 MET cc_start: 0.6960 (mmm) cc_final: 0.6430 (mmt) REVERT: A 192 ASP cc_start: 0.8392 (t70) cc_final: 0.8029 (t0) REVERT: A 213 MET cc_start: 0.8885 (mmm) cc_final: 0.7903 (mmm) REVERT: A 229 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8469 (mm-40) REVERT: B 49 MET cc_start: 0.8556 (ptt) cc_final: 0.8010 (pp-130) REVERT: C 137 MET cc_start: 0.9134 (mpp) cc_final: 0.8891 (mmp) REVERT: C 185 GLN cc_start: 0.8713 (pm20) cc_final: 0.8496 (pm20) REVERT: E 148 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7796 (mm-40) REVERT: E 153 GLU cc_start: 0.8862 (tp30) cc_final: 0.8486 (tp30) REVERT: E 207 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8404 (tpt-90) REVERT: E 429 ILE cc_start: 0.8350 (mp) cc_final: 0.8125 (mt) REVERT: D 15 PHE cc_start: 0.8291 (m-80) cc_final: 0.7998 (t80) REVERT: D 229 GLN cc_start: 0.8891 (tp40) cc_final: 0.8638 (tp40) REVERT: K 18 HIS cc_start: 0.7085 (m90) cc_final: 0.6675 (m-70) REVERT: L 32 ILE cc_start: 0.8096 (tt) cc_final: 0.7880 (pt) outliers start: 19 outliers final: 13 residues processed: 164 average time/residue: 0.5340 time to fit residues: 97.9679 Evaluate side-chains 160 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL 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 C residue 111 VAL 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 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 152 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.080872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061089 restraints weight = 41491.955| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.35 r_work: 0.2904 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 16191 Z= 0.197 Angle : 0.707 12.219 22054 Z= 0.339 Chirality : 0.045 0.264 2537 Planarity : 0.004 0.042 2704 Dihedral : 8.484 103.594 2598 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.12 % Allowed : 17.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1887 helix: 2.30 (0.20), residues: 618 sheet: -0.86 (0.23), residues: 492 loop : -0.81 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 33 TYR 0.024 0.001 TYR E 299 PHE 0.018 0.001 PHE D 304 TRP 0.020 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00458 (16146) covalent geometry : angle 0.69065 (21949) SS BOND : bond 0.00580 ( 21) SS BOND : angle 2.64562 ( 42) hydrogen bonds : bond 0.03815 ( 637) hydrogen bonds : angle 4.62239 ( 1797) metal coordination : bond 0.00195 ( 3) link_ALPHA1-3 : bond 0.00993 ( 4) link_ALPHA1-3 : angle 3.28013 ( 12) link_ALPHA1-6 : bond 0.01210 ( 4) link_ALPHA1-6 : angle 1.58527 ( 12) link_BETA1-4 : bond 0.00573 ( 7) link_BETA1-4 : angle 1.52997 ( 21) link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 1.79532 ( 18) ********************** 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 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 452 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8818 (tptp) REVERT: F 501 TYR cc_start: 0.8263 (m-80) cc_final: 0.8034 (m-80) REVERT: A 112 MET cc_start: 0.7166 (mmm) cc_final: 0.6799 (mmp) REVERT: A 192 ASP cc_start: 0.8411 (t70) cc_final: 0.8054 (t0) REVERT: A 213 MET cc_start: 0.8927 (mmm) cc_final: 0.8003 (mmm) REVERT: A 229 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8496 (mm-40) REVERT: B 49 MET cc_start: 0.8557 (ptt) cc_final: 0.7996 (pp-130) REVERT: C 137 MET cc_start: 0.9207 (mpp) cc_final: 0.8886 (mmp) REVERT: C 153 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: C 185 GLN cc_start: 0.8725 (pm20) cc_final: 0.8512 (pm20) REVERT: E 153 GLU cc_start: 0.8871 (tp30) cc_final: 0.8506 (tp30) REVERT: E 274 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8520 (mmtt) REVERT: D 15 PHE cc_start: 0.8361 (m-80) cc_final: 0.8078 (t80) REVERT: K 18 HIS cc_start: 0.7252 (m90) cc_final: 0.6828 (m-70) outliers start: 19 outliers final: 17 residues processed: 153 average time/residue: 0.5680 time to fit residues: 96.8878 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 460 ASP 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 E residue 238 VAL Chi-restraints excluded: chain D residue 112 MET 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 51 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.080386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060636 restraints weight = 41219.163| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.33 r_work: 0.2896 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 16191 Z= 0.197 Angle : 0.716 12.691 22054 Z= 0.343 Chirality : 0.045 0.257 2537 Planarity : 0.004 0.044 2704 Dihedral : 8.435 103.013 2598 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.24 % Allowed : 17.19 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1887 helix: 2.26 (0.20), residues: 617 sheet: -1.02 (0.23), residues: 503 loop : -0.82 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 33 TYR 0.023 0.002 TYR E 299 PHE 0.017 0.001 PHE D 304 TRP 0.030 0.001 TRP F 440 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00457 (16146) covalent geometry : angle 0.69829 (21949) SS BOND : bond 0.00564 ( 21) SS BOND : angle 2.78619 ( 42) hydrogen bonds : bond 0.04023 ( 637) hydrogen bonds : angle 4.69940 ( 1797) metal coordination : bond 0.00055 ( 3) link_ALPHA1-3 : bond 0.00984 ( 4) link_ALPHA1-3 : angle 3.26399 ( 12) link_ALPHA1-6 : bond 0.01204 ( 4) link_ALPHA1-6 : angle 1.65100 ( 12) link_BETA1-4 : bond 0.00576 ( 7) link_BETA1-4 : angle 1.50091 ( 21) link_NAG-ASN : bond 0.00183 ( 6) link_NAG-ASN : angle 1.79088 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.31 seconds wall clock time: 72 minutes 54.68 seconds (4374.68 seconds total)