Starting phenix.real_space_refine on Fri Jul 3 09:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2026/5bkf_9403.cif" } resolution = 3.6 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8785 2.51 5 N 2125 2.21 5 O 2473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2667 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2667 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2661 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2660 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.50, per 1000 atoms: 0.26 Number of scatterers: 13470 At special positions: 0 Unit cell: (92.96, 91.3, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2473 8.00 N 2125 7.00 C 8785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 205 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 594.6 milliseconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 38.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 Processing helix chain 'A' and resid 78 through 81 removed outlier: 3.505A pdb=" N ALA A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.953A pdb=" N ASP A 98 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 5.007A pdb=" N ILE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.681A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 316 removed outlier: 3.551A pdb=" N ARG A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 416 Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 78 through 81 removed outlier: 3.747A pdb=" N ALA B 81 " --> pdb=" O SER B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 93 through 100 removed outlier: 4.061A pdb=" N ASP B 98 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 removed outlier: 5.173A pdb=" N ILE B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 255 through 280 removed outlier: 3.813A pdb=" N ARG B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 316 Processing helix chain 'B' and resid 384 through 416 Proline residue: B 400 - end of helix Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 93 through 100 removed outlier: 4.027A pdb=" N ASP C 98 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 removed outlier: 5.050A pdb=" N ILE C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Proline residue: C 237 - end of helix Processing helix chain 'C' and resid 255 through 280 Processing helix chain 'C' and resid 288 through 315 Processing helix chain 'C' and resid 384 through 414 Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.883A pdb=" N GLY D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 93 through 100 removed outlier: 4.186A pdb=" N ASP D 98 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 99 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 235 through 248 Processing helix chain 'D' and resid 255 through 280 Processing helix chain 'D' and resid 288 through 316 removed outlier: 3.698A pdb=" N ARG D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 416 Proline residue: D 400 - end of helix removed outlier: 3.538A pdb=" N ILE D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.732A pdb=" N THR E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 298 removed outlier: 3.921A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.552A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 474 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.047A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.047A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N GLN A 184 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 50 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 59 removed outlier: 4.292A pdb=" N VAL A 58 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A 64 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER A 144 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A 110 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.664A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.785A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 114 removed outlier: 6.178A pdb=" N GLU B 110 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B 144 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 112 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N GLN B 184 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE B 50 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 107 removed outlier: 3.809A pdb=" N GLU B 224 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AB1, first strand: chain 'C' and resid 174 through 177 removed outlier: 6.498A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 51 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY C 112 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER C 144 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU C 110 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 59 Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.706A pdb=" N GLU C 224 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.607A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL D 44 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLU D 176 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 46 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.083A pdb=" N GLU D 110 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER D 144 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 106 through 107 removed outlier: 3.522A pdb=" N GLU D 201 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D 222 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU D 199 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLU D 224 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LYS D 197 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.488A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN E 130 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER E 128 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER E 160 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU E 126 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 105 through 107 removed outlier: 6.017A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AC3, first strand: chain 'E' and resid 224 through 225 removed outlier: 3.553A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2127 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: 2.39 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4139 1.34 - 1.46: 3544 1.46 - 1.58: 5979 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 13804 Sorted by residual: bond pdb=" N TYR D 235 " pdb=" CA TYR D 235 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.27e-02 6.20e+03 6.70e+00 bond pdb=" N GLN C 157 " pdb=" CA GLN C 157 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.57e+00 bond pdb=" N TYR C 235 " pdb=" CA TYR C 235 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" N LYS D 213 " pdb=" CA LYS D 213 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.23e-02 6.61e+03 6.16e+00 bond pdb=" N THR D 211 " pdb=" CA THR D 211 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 ... (remaining 13799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 18107 1.18 - 2.35: 537 2.35 - 3.53: 94 3.53 - 4.70: 49 4.70 - 5.88: 12 Bond angle restraints: 18799 Sorted by residual: angle pdb=" CA GLY D 212 " pdb=" C GLY D 212 " pdb=" O GLY D 212 " ideal model delta sigma weight residual 121.56 118.26 3.30 1.07e+00 8.73e-01 9.49e+00 angle pdb=" CA THR D 211 " pdb=" C THR D 211 " pdb=" O THR D 211 " ideal model delta sigma weight residual 120.82 117.67 3.15 1.05e+00 9.07e-01 9.02e+00 angle pdb=" N THR D 119 " pdb=" CA THR D 119 " pdb=" CB THR D 119 " ideal model delta sigma weight residual 114.17 110.87 3.30 1.14e+00 7.69e-01 8.37e+00 angle pdb=" N CYS E 221 " pdb=" CA CYS E 221 " pdb=" C CYS E 221 " ideal model delta sigma weight residual 114.56 111.05 3.51 1.27e+00 6.20e-01 7.66e+00 angle pdb=" N THR A 120 " pdb=" CA THR A 120 " pdb=" C THR A 120 " ideal model delta sigma weight residual 110.80 105.50 5.30 2.13e+00 2.20e-01 6.20e+00 ... (remaining 18794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7353 17.94 - 35.88: 608 35.88 - 53.82: 103 53.82 - 71.77: 13 71.77 - 89.71: 9 Dihedral angle restraints: 8086 sinusoidal: 3092 harmonic: 4994 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -174.13 88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 50.70 42.30 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" CB CYS D 145 " pdb=" SG CYS D 145 " pdb=" SG CYS D 159 " pdb=" CB CYS D 159 " ideal model delta sinusoidal sigma weight residual 93.00 52.89 40.11 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 8083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1616 0.039 - 0.079: 378 0.079 - 0.118: 172 0.118 - 0.157: 15 0.157 - 0.196: 6 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 45 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 2184 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 408 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ILE A 408 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 408 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 409 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 408 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C ILE C 408 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE C 408 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE C 409 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 156 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C VAL C 156 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 156 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN C 157 " -0.008 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 165 2.59 - 3.17: 12413 3.17 - 3.75: 20340 3.75 - 4.32: 28593 4.32 - 4.90: 47968 Nonbonded interactions: 109479 Sorted by model distance: nonbonded pdb=" O VAL D 118 " pdb=" OG1 THR D 119 " model vdw 2.015 3.040 nonbonded pdb=" O VAL E 134 " pdb=" OG1 THR E 135 " model vdw 2.086 3.040 nonbonded pdb=" O VAL C 118 " pdb=" OG1 THR C 119 " model vdw 2.089 3.040 nonbonded pdb=" O VAL B 118 " pdb=" OG1 THR B 119 " model vdw 2.089 3.040 nonbonded pdb=" NH1 ARG E 50 " pdb=" O PRO E 51 " model vdw 2.161 3.120 ... (remaining 109474 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 15 through 384 or (resid 385 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 or (resid 392 through 398 a \ nd (name N or name CA or name C or name O or name CB )) or resid 399 through 503 \ )) selection = (chain 'B' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 384 or (resid 385 through 390 and \ (name N or name CA or name C or name O or name CB )) or resid 391 through 417 or \ (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 1 through 503)) selection = (chain 'C' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 392 or (resid 393 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 503)) selection = (chain 'D' and (resid 15 through 385 or (resid 386 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 392 or (resid 393 t \ hrough 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.060 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13823 Z= 0.189 Angle : 0.579 13.537 18846 Z= 0.293 Chirality : 0.041 0.196 2187 Planarity : 0.003 0.031 2338 Dihedral : 13.372 89.708 4816 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.35 % Allowed : 1.87 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.64 (0.18), residues: 1669 helix: -0.87 (0.19), residues: 578 sheet: -3.85 (0.20), residues: 394 loop : -2.73 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.017 0.001 TYR C 308 PHE 0.009 0.001 PHE D 214 TRP 0.006 0.001 TRP A 75 HIS 0.003 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (13804) covalent geometry : angle 0.54132 / 0.28 (18799) SS BOND : bond 0.00282 / 0.21 ( 10) SS BOND : angle 1.43137 / 0.77 ( 20) hydrogen bonds : bond 0.16505 / 11.05 ( 666) hydrogen bonds : angle 8.07071 / 5.43 ( 2127) link_NAG-ASN : bond 0.00580 / 0.31 ( 9) link_NAG-ASN : angle 5.35454 / 3.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8228 (p0) cc_final: 0.8024 (p0) REVERT: A 218 GLU cc_start: 0.7431 (pt0) cc_final: 0.6486 (pt0) REVERT: A 286 TYR cc_start: 0.8295 (p90) cc_final: 0.8033 (p90) REVERT: B 232 ILE cc_start: 0.8081 (tp) cc_final: 0.7832 (mt) REVERT: C 23 LYS cc_start: 0.8446 (tttt) cc_final: 0.7869 (tptt) REVERT: D 250 TRP cc_start: 0.7389 (m100) cc_final: 0.7181 (m100) REVERT: E 90 ASN cc_start: 0.6878 (m-40) cc_final: 0.6568 (m-40) REVERT: E 300 LYS cc_start: 0.8249 (mttt) cc_final: 0.7999 (mttt) REVERT: E 329 GLN cc_start: 0.8324 (tp40) cc_final: 0.7986 (tp40) outliers start: 5 outliers final: 1 residues processed: 276 average time/residue: 0.1075 time to fit residues: 43.0559 Evaluate side-chains 190 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 220 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 233 GLN A 273 GLN A 312 ASN B 73 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 82 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136303 restraints weight = 18999.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140431 restraints weight = 9479.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143073 restraints weight = 5755.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144852 restraints weight = 4007.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145997 restraints weight = 3066.959| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13823 Z= 0.131 Angle : 0.672 13.048 18846 Z= 0.330 Chirality : 0.045 0.187 2187 Planarity : 0.004 0.050 2338 Dihedral : 5.411 81.188 1816 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 8.59 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.20), residues: 1669 helix: 1.16 (0.21), residues: 563 sheet: -3.00 (0.24), residues: 352 loop : -2.08 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 190 TYR 0.021 0.002 TYR B 308 PHE 0.019 0.002 PHE C 51 TRP 0.011 0.001 TRP A 177 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13804) covalent geometry : angle 0.63852 / 0.32 (18799) SS BOND : bond 0.00551 / 0.32 ( 10) SS BOND : angle 1.88915 / 1.17 ( 20) hydrogen bonds : bond 0.03785 / 2.53 ( 666) hydrogen bonds : angle 4.89155 / 3.36 ( 2127) link_NAG-ASN : bond 0.00874 / 0.46 ( 9) link_NAG-ASN : angle 5.34356 / 3.42 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7948 (mtpp) REVERT: B 281 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7451 (tp) REVERT: C 23 LYS cc_start: 0.8496 (tttt) cc_final: 0.7883 (tptt) REVERT: D 250 TRP cc_start: 0.7538 (m100) cc_final: 0.7264 (m100) REVERT: D 270 MET cc_start: 0.8270 (mmm) cc_final: 0.7914 (mmm) REVERT: E 56 ILE cc_start: 0.8493 (mp) cc_final: 0.8273 (mt) REVERT: E 90 ASN cc_start: 0.7131 (m-40) cc_final: 0.6874 (m-40) REVERT: E 190 ARG cc_start: 0.7098 (ttm110) cc_final: 0.6561 (mtt180) REVERT: E 300 LYS cc_start: 0.8265 (mttt) cc_final: 0.8002 (mttt) REVERT: E 329 GLN cc_start: 0.8341 (tp40) cc_final: 0.7506 (tp40) outliers start: 25 outliers final: 11 residues processed: 207 average time/residue: 0.0975 time to fit residues: 30.4029 Evaluate side-chains 174 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 273 GLN A 312 ASN D 73 GLN D 157 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117490 restraints weight = 20219.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121228 restraints weight = 10111.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123653 restraints weight = 6271.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125225 restraints weight = 4458.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126298 restraints weight = 3512.082| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13823 Z= 0.290 Angle : 0.769 14.224 18846 Z= 0.382 Chirality : 0.049 0.369 2187 Planarity : 0.005 0.048 2338 Dihedral : 6.186 88.939 1814 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.84 % Allowed : 12.47 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.64 (0.20), residues: 1669 helix: 0.98 (0.21), residues: 583 sheet: -2.65 (0.25), residues: 360 loop : -1.94 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 48 TYR 0.023 0.002 TYR B 308 PHE 0.019 0.002 PHE A 55 TRP 0.018 0.002 TRP A 177 HIS 0.004 0.002 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (13804) covalent geometry : angle 0.73894 / 0.38 (18799) SS BOND : bond 0.00557 / 0.30 ( 10) SS BOND : angle 1.53026 / 0.88 ( 20) hydrogen bonds : bond 0.04409 / 2.95 ( 666) hydrogen bonds : angle 5.02856 / 3.45 ( 2127) link_NAG-ASN : bond 0.00750 / 0.40 ( 9) link_NAG-ASN : angle 5.59966 / 3.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7714 (t0) cc_final: 0.7431 (t0) REVERT: A 226 GLN cc_start: 0.8319 (pt0) cc_final: 0.7941 (pt0) REVERT: A 230 TYR cc_start: 0.8216 (m-80) cc_final: 0.7618 (m-80) REVERT: A 253 MET cc_start: 0.7288 (ptp) cc_final: 0.7028 (ptp) REVERT: B 270 MET cc_start: 0.8713 (tpp) cc_final: 0.8221 (tpp) REVERT: C 23 LYS cc_start: 0.8603 (tttt) cc_final: 0.8011 (tptt) REVERT: D 104 ASP cc_start: 0.8417 (t0) cc_final: 0.8199 (m-30) REVERT: D 240 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7621 (mp) REVERT: E 257 LEU cc_start: 0.8430 (tp) cc_final: 0.7816 (mp) REVERT: E 300 LYS cc_start: 0.8423 (mttt) cc_final: 0.8160 (mttt) REVERT: E 329 GLN cc_start: 0.8719 (tp40) cc_final: 0.7943 (tp40) outliers start: 41 outliers final: 27 residues processed: 259 average time/residue: 0.0949 time to fit residues: 37.0761 Evaluate side-chains 217 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123685 restraints weight = 19978.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127532 restraints weight = 10007.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130021 restraints weight = 6192.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131660 restraints weight = 4402.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132770 restraints weight = 3445.058| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13823 Z= 0.140 Angle : 0.659 11.814 18846 Z= 0.321 Chirality : 0.045 0.216 2187 Planarity : 0.004 0.046 2338 Dihedral : 5.691 85.075 1814 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.56 % Allowed : 16.76 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.21), residues: 1669 helix: 1.30 (0.22), residues: 583 sheet: -2.33 (0.26), residues: 360 loop : -1.66 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 190 TYR 0.032 0.002 TYR D 308 PHE 0.019 0.001 PHE C 406 TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13804) covalent geometry : angle 0.63185 / 0.31 (18799) SS BOND : bond 0.00421 / 0.24 ( 10) SS BOND : angle 1.47473 / 0.85 ( 20) hydrogen bonds : bond 0.03697 / 2.50 ( 666) hydrogen bonds : angle 4.62965 / 3.18 ( 2127) link_NAG-ASN : bond 0.00803 / 0.42 ( 9) link_NAG-ASN : angle 4.87058 / 3.12 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8538 (t0) cc_final: 0.8222 (t0) REVERT: A 220 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8331 (mttm) REVERT: B 217 ILE cc_start: 0.8288 (mm) cc_final: 0.8058 (mt) REVERT: C 23 LYS cc_start: 0.8522 (tttt) cc_final: 0.7970 (tptt) REVERT: C 278 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7280 (mtm180) REVERT: D 104 ASP cc_start: 0.8332 (t0) cc_final: 0.8131 (m-30) REVERT: E 190 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6744 (mtt180) REVERT: E 300 LYS cc_start: 0.8398 (mttt) cc_final: 0.8127 (mttt) outliers start: 37 outliers final: 26 residues processed: 240 average time/residue: 0.0937 time to fit residues: 33.3040 Evaluate side-chains 214 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123106 restraints weight = 19986.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127043 restraints weight = 9981.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129596 restraints weight = 6146.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131288 restraints weight = 4330.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132403 restraints weight = 3380.466| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13823 Z= 0.139 Angle : 0.638 10.778 18846 Z= 0.313 Chirality : 0.044 0.240 2187 Planarity : 0.004 0.043 2338 Dihedral : 5.474 79.629 1814 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.60 % Allowed : 16.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.21), residues: 1669 helix: 1.48 (0.22), residues: 579 sheet: -2.13 (0.26), residues: 360 loop : -1.57 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.031 0.002 TYR E 325 PHE 0.018 0.001 PHE C 406 TRP 0.011 0.001 TRP A 177 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13804) covalent geometry : angle 0.61249 / 0.31 (18799) SS BOND : bond 0.00397 / 0.23 ( 10) SS BOND : angle 1.28048 / 0.76 ( 20) hydrogen bonds : bond 0.03487 / 2.35 ( 666) hydrogen bonds : angle 4.47746 / 3.08 ( 2127) link_NAG-ASN : bond 0.00792 / 0.42 ( 9) link_NAG-ASN : angle 4.62252 / 3.00 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.7564 (m) cc_final: 0.7296 (t) REVERT: A 220 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8369 (mttm) REVERT: B 32 ASP cc_start: 0.7861 (p0) cc_final: 0.7660 (p0) REVERT: B 217 ILE cc_start: 0.8179 (mm) cc_final: 0.7907 (tt) REVERT: C 23 LYS cc_start: 0.8539 (tttt) cc_final: 0.8006 (tptt) REVERT: C 25 MET cc_start: 0.8046 (ptp) cc_final: 0.7545 (ptt) REVERT: D 313 PHE cc_start: 0.7750 (t80) cc_final: 0.7362 (t80) REVERT: E 300 LYS cc_start: 0.8493 (mttt) cc_final: 0.8056 (mttt) outliers start: 52 outliers final: 36 residues processed: 234 average time/residue: 0.0936 time to fit residues: 33.3237 Evaluate side-chains 225 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119995 restraints weight = 20153.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123896 restraints weight = 9907.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126427 restraints weight = 6066.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128074 restraints weight = 4268.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129079 restraints weight = 3326.636| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13823 Z= 0.182 Angle : 0.674 10.312 18846 Z= 0.331 Chirality : 0.045 0.259 2187 Planarity : 0.004 0.043 2338 Dihedral : 5.517 75.852 1814 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.81 % Allowed : 18.21 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.21), residues: 1669 helix: 1.52 (0.22), residues: 579 sheet: -2.08 (0.26), residues: 362 loop : -1.53 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 190 TYR 0.033 0.002 TYR D 308 PHE 0.017 0.002 PHE C 406 TRP 0.017 0.001 TRP E 471 HIS 0.002 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13804) covalent geometry : angle 0.65072 / 0.33 (18799) SS BOND : bond 0.00777 / 0.30 ( 10) SS BOND : angle 1.54750 / 1.00 ( 20) hydrogen bonds : bond 0.03610 / 2.44 ( 666) hydrogen bonds : angle 4.54308 / 3.11 ( 2127) link_NAG-ASN : bond 0.00620 / 0.33 ( 9) link_NAG-ASN : angle 4.55039 / 2.99 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8563 (t0) cc_final: 0.8353 (t0) REVERT: A 171 ASN cc_start: 0.7682 (t0) cc_final: 0.7426 (t0) REVERT: A 220 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8377 (mtmm) REVERT: A 226 GLN cc_start: 0.8286 (pt0) cc_final: 0.8069 (pt0) REVERT: B 120 THR cc_start: 0.8866 (t) cc_final: 0.8545 (m) REVERT: B 154 MET cc_start: 0.7481 (mpp) cc_final: 0.7237 (ptp) REVERT: B 217 ILE cc_start: 0.8320 (mm) cc_final: 0.8086 (tt) REVERT: C 23 LYS cc_start: 0.8569 (tttt) cc_final: 0.8018 (tptt) REVERT: C 218 GLU cc_start: 0.7682 (tt0) cc_final: 0.7436 (tt0) REVERT: C 270 MET cc_start: 0.8112 (mmm) cc_final: 0.6955 (mmt) REVERT: C 307 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 313 PHE cc_start: 0.7853 (t80) cc_final: 0.7454 (t80) REVERT: E 114 LYS cc_start: 0.8590 (pttt) cc_final: 0.8318 (mmtt) REVERT: E 190 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6659 (mtt180) REVERT: E 257 LEU cc_start: 0.8423 (tp) cc_final: 0.7799 (mp) outliers start: 55 outliers final: 43 residues processed: 243 average time/residue: 0.0910 time to fit residues: 33.4742 Evaluate side-chains 240 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118184 restraints weight = 20121.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122071 restraints weight = 9916.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124571 restraints weight = 6071.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126258 restraints weight = 4288.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127289 restraints weight = 3331.627| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13823 Z= 0.197 Angle : 0.688 9.649 18846 Z= 0.338 Chirality : 0.046 0.337 2187 Planarity : 0.004 0.043 2338 Dihedral : 5.461 69.030 1814 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.81 % Allowed : 19.18 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.21), residues: 1669 helix: 1.47 (0.22), residues: 583 sheet: -2.06 (0.25), residues: 400 loop : -1.40 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.030 0.002 TYR D 308 PHE 0.018 0.002 PHE C 406 TRP 0.013 0.001 TRP E 471 HIS 0.002 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (13804) covalent geometry : angle 0.66470 / 0.33 (18799) SS BOND : bond 0.00490 / 0.27 ( 10) SS BOND : angle 1.89783 / 0.96 ( 20) hydrogen bonds : bond 0.03614 / 2.43 ( 666) hydrogen bonds : angle 4.55881 / 3.11 ( 2127) link_NAG-ASN : bond 0.00626 / 0.33 ( 9) link_NAG-ASN : angle 4.48784 / 2.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8638 (t0) cc_final: 0.8412 (t0) REVERT: A 171 ASN cc_start: 0.7678 (t0) cc_final: 0.7391 (t0) REVERT: A 220 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8375 (mtmm) REVERT: A 243 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 120 THR cc_start: 0.8890 (t) cc_final: 0.8562 (m) REVERT: B 217 ILE cc_start: 0.8375 (mm) cc_final: 0.8149 (tt) REVERT: C 23 LYS cc_start: 0.8584 (tttt) cc_final: 0.8033 (tptt) REVERT: C 218 GLU cc_start: 0.7686 (tt0) cc_final: 0.7460 (tt0) REVERT: D 240 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7420 (mp) REVERT: D 313 PHE cc_start: 0.7861 (t80) cc_final: 0.7455 (t80) REVERT: D 405 ILE cc_start: 0.8085 (tt) cc_final: 0.7757 (tp) REVERT: E 114 LYS cc_start: 0.8633 (pttt) cc_final: 0.8373 (mmtt) REVERT: E 190 ARG cc_start: 0.7452 (ttm110) cc_final: 0.6668 (mtt180) REVERT: E 257 LEU cc_start: 0.8476 (tp) cc_final: 0.7837 (mp) REVERT: E 302 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8770 (t) outliers start: 55 outliers final: 44 residues processed: 246 average time/residue: 0.0942 time to fit residues: 35.2103 Evaluate side-chains 253 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121878 restraints weight = 20075.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125885 restraints weight = 9831.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128491 restraints weight = 6001.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130133 restraints weight = 4225.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131346 restraints weight = 3313.379| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13823 Z= 0.136 Angle : 0.654 10.775 18846 Z= 0.318 Chirality : 0.044 0.275 2187 Planarity : 0.004 0.042 2338 Dihedral : 5.117 67.197 1814 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.32 % Allowed : 20.01 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.21), residues: 1669 helix: 1.63 (0.22), residues: 583 sheet: -1.99 (0.24), residues: 417 loop : -1.26 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.029 0.001 TYR D 308 PHE 0.019 0.001 PHE C 406 TRP 0.011 0.001 TRP E 471 HIS 0.002 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13804) covalent geometry : angle 0.63269 / 0.31 (18799) SS BOND : bond 0.00517 / 0.25 ( 10) SS BOND : angle 2.06229 / 1.27 ( 20) hydrogen bonds : bond 0.03379 / 2.27 ( 666) hydrogen bonds : angle 4.40631 / 3.01 ( 2127) link_NAG-ASN : bond 0.00645 / 0.34 ( 9) link_NAG-ASN : angle 4.08250 / 2.69 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7412 (mp) REVERT: B 120 THR cc_start: 0.8653 (t) cc_final: 0.8420 (m) REVERT: C 23 LYS cc_start: 0.8572 (tttt) cc_final: 0.7981 (tptt) REVERT: C 270 MET cc_start: 0.8035 (mmm) cc_final: 0.6931 (mmt) REVERT: D 240 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7271 (mp) REVERT: D 268 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7412 (tp) REVERT: D 313 PHE cc_start: 0.7831 (t80) cc_final: 0.7425 (t80) REVERT: E 32 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7122 (m110) REVERT: E 190 ARG cc_start: 0.7387 (ttm110) cc_final: 0.6708 (mtt180) REVERT: E 257 LEU cc_start: 0.8328 (tp) cc_final: 0.7741 (mp) REVERT: E 302 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8690 (t) outliers start: 48 outliers final: 36 residues processed: 234 average time/residue: 0.0859 time to fit residues: 30.7443 Evaluate side-chains 230 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124252 restraints weight = 20026.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128260 restraints weight = 9855.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130872 restraints weight = 6030.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132515 restraints weight = 4244.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133726 restraints weight = 3322.885| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13823 Z= 0.124 Angle : 0.641 10.625 18846 Z= 0.313 Chirality : 0.044 0.273 2187 Planarity : 0.004 0.041 2338 Dihedral : 4.885 65.889 1814 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.05 % Allowed : 21.33 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.21), residues: 1669 helix: 1.76 (0.22), residues: 583 sheet: -1.84 (0.25), residues: 415 loop : -1.11 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.028 0.001 TYR D 308 PHE 0.018 0.001 PHE C 406 TRP 0.010 0.001 TRP A 177 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13804) covalent geometry : angle 0.62142 / 0.31 (18799) SS BOND : bond 0.00381 / 0.22 ( 10) SS BOND : angle 1.79245 / 1.09 ( 20) hydrogen bonds : bond 0.03271 / 2.20 ( 666) hydrogen bonds : angle 4.26771 / 2.90 ( 2127) link_NAG-ASN : bond 0.00600 / 0.32 ( 9) link_NAG-ASN : angle 3.88953 / 2.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.6891 (mmpt) cc_final: 0.6482 (mttp) REVERT: A 243 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 270 MET cc_start: 0.7944 (tpp) cc_final: 0.7459 (mpp) REVERT: B 120 THR cc_start: 0.8582 (t) cc_final: 0.8297 (m) REVERT: C 23 LYS cc_start: 0.8588 (tttt) cc_final: 0.8007 (tptt) REVERT: C 270 MET cc_start: 0.8030 (mmm) cc_final: 0.7464 (mmm) REVERT: D 268 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7422 (tp) REVERT: D 313 PHE cc_start: 0.7777 (t80) cc_final: 0.7420 (t80) REVERT: E 32 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7207 (m110) REVERT: E 190 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6701 (mtt180) REVERT: E 302 SER cc_start: 0.8810 (p) cc_final: 0.8601 (p) outliers start: 44 outliers final: 36 residues processed: 238 average time/residue: 0.0931 time to fit residues: 33.4149 Evaluate side-chains 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 134 optimal weight: 0.0040 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130408 restraints weight = 20047.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134278 restraints weight = 10084.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136783 restraints weight = 6264.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138411 restraints weight = 4476.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139542 restraints weight = 3524.524| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13823 Z= 0.136 Angle : 0.681 16.512 18846 Z= 0.326 Chirality : 0.044 0.278 2187 Planarity : 0.004 0.067 2338 Dihedral : 4.865 64.471 1814 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.05 % Allowed : 21.61 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.21), residues: 1669 helix: 1.81 (0.22), residues: 582 sheet: -1.81 (0.25), residues: 413 loop : -1.10 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 34 TYR 0.028 0.001 TYR D 308 PHE 0.019 0.001 PHE B 313 TRP 0.010 0.001 TRP A 177 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13804) covalent geometry : angle 0.64032 / 0.32 (18799) SS BOND : bond 0.00383 / 0.21 ( 10) SS BOND : angle 1.74122 / 1.06 ( 20) hydrogen bonds : bond 0.03305 / 2.22 ( 666) hydrogen bonds : angle 4.25067 / 2.88 ( 2127) link_NAG-ASN : bond 0.00570 / 0.30 ( 9) link_NAG-ASN : angle 6.01615 / 3.17 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.6834 (mmpt) cc_final: 0.6454 (mttp) REVERT: A 243 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7294 (mp) REVERT: A 270 MET cc_start: 0.7939 (tpp) cc_final: 0.7471 (mpp) REVERT: B 120 THR cc_start: 0.8554 (t) cc_final: 0.8307 (m) REVERT: C 19 ASP cc_start: 0.6941 (t70) cc_final: 0.6578 (t0) REVERT: C 23 LYS cc_start: 0.8601 (tttt) cc_final: 0.7987 (tptt) REVERT: C 270 MET cc_start: 0.7995 (mmm) cc_final: 0.7471 (mmm) REVERT: D 154 MET cc_start: 0.8693 (mpp) cc_final: 0.8316 (mpp) REVERT: D 240 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7264 (mp) REVERT: D 268 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7424 (tp) REVERT: D 313 PHE cc_start: 0.7784 (t80) cc_final: 0.7429 (t80) REVERT: E 32 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7143 (m-40) REVERT: E 174 ARG cc_start: 0.6993 (mtp85) cc_final: 0.6779 (mtp180) REVERT: E 190 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6715 (mtt180) outliers start: 44 outliers final: 33 residues processed: 230 average time/residue: 0.0965 time to fit residues: 33.4557 Evaluate side-chains 228 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130791 restraints weight = 20192.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134636 restraints weight = 10133.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137138 restraints weight = 6303.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138704 restraints weight = 4494.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139855 restraints weight = 3556.252| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13823 Z= 0.135 Angle : 0.662 13.295 18846 Z= 0.319 Chirality : 0.044 0.275 2187 Planarity : 0.004 0.066 2338 Dihedral : 4.830 62.919 1814 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.91 % Allowed : 21.68 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.21), residues: 1669 helix: 1.86 (0.22), residues: 582 sheet: -1.75 (0.25), residues: 413 loop : -1.03 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 34 TYR 0.027 0.001 TYR D 308 PHE 0.017 0.001 PHE C 406 TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13804) covalent geometry : angle 0.63099 / 0.31 (18799) SS BOND : bond 0.00386 / 0.22 ( 10) SS BOND : angle 1.72612 / 1.05 ( 20) hydrogen bonds : bond 0.03274 / 2.21 ( 666) hydrogen bonds : angle 4.22757 / 2.86 ( 2127) link_NAG-ASN : bond 0.00553 / 0.29 ( 9) link_NAG-ASN : angle 5.12785 / 2.89 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.88 seconds wall clock time: 31 minutes 34.70 seconds (1894.70 seconds total)