Starting phenix.real_space_refine on Wed Mar 4 11:42:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkf_9403/03_2026/5bkf_9403.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkf_9403/03_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_9403/03_2026/5bkf_9403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkf_9403/03_2026/5bkf_9403.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkf_9403/03_2026/5bkf_9403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkf_9403/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.14, per 1000 atoms: 0.23 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: 1.11 Conformation dependent library (CDL) restraints added in 630.6 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: 0.49 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: 2.45 Time building geometry restraints manager: 1.50 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 - 21.74: 7750 21.74 - 43.47: 455 43.47 - 65.21: 47 65.21 - 86.95: 14 86.95 - 108.69: 9 Dihedral angle restraints: 8275 sinusoidal: 3281 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 8272 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 14.141 108.685 5005 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 covalent geometry : bond 0.00426 (13804) covalent geometry : angle 0.54132 (18799) SS BOND : bond 0.00282 ( 10) SS BOND : angle 1.43137 ( 20) hydrogen bonds : bond 0.16505 ( 666) hydrogen bonds : angle 8.07071 ( 2127) link_NAG-ASN : bond 0.00580 ( 9) link_NAG-ASN : angle 5.35454 ( 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 : 0.477 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: 0.1248 time to fit residues: 49.4858 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 : 0.501 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3840 r_free = 0.3840 target = 0.154307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136080 restraints weight = 19035.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140214 restraints weight = 9521.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142871 restraints weight = 5788.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144619 restraints weight = 4023.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145782 restraints weight = 3086.301| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13823 Z= 0.132 Angle : 0.676 13.448 18846 Z= 0.332 Chirality : 0.045 0.181 2187 Planarity : 0.004 0.052 2338 Dihedral : 7.681 82.264 2005 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.73 % Allowed : 8.66 % Favored : 89.61 % 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: -1.85 (0.20), residues: 1669 helix: 1.08 (0.21), residues: 563 sheet: -3.02 (0.24), residues: 352 loop : -2.10 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 190 TYR 0.022 0.001 TYR B 308 PHE 0.018 0.001 PHE C 51 TRP 0.011 0.001 TRP A 177 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00290 (13804) covalent geometry : angle 0.64002 (18799) SS BOND : bond 0.00876 ( 10) SS BOND : angle 2.07497 ( 20) hydrogen bonds : bond 0.03877 ( 666) hydrogen bonds : angle 4.96393 ( 2127) link_NAG-ASN : bond 0.00847 ( 9) link_NAG-ASN : angle 5.56429 ( 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 214 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: B 281 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7449 (tp) REVERT: C 23 LYS cc_start: 0.8463 (tttt) cc_final: 0.7856 (tptt) REVERT: D 250 TRP cc_start: 0.7525 (m100) cc_final: 0.7248 (m100) REVERT: E 90 ASN cc_start: 0.7112 (m-40) cc_final: 0.6854 (m-40) REVERT: E 190 ARG cc_start: 0.7083 (ttm110) cc_final: 0.6520 (mtt180) REVERT: E 266 PHE cc_start: 0.8069 (m-80) cc_final: 0.7862 (m-80) REVERT: E 300 LYS cc_start: 0.8262 (mttt) cc_final: 0.8003 (mttt) REVERT: E 329 GLN cc_start: 0.8346 (tp40) cc_final: 0.7735 (tp40) outliers start: 25 outliers final: 11 residues processed: 205 average time/residue: 0.1106 time to fit residues: 34.1176 Evaluate side-chains 175 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 19 ASP 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 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: 3.9990 chunk 17 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3594 r_free = 0.3594 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114855 restraints weight = 20536.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118574 restraints weight = 10465.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120976 restraints weight = 6581.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122545 restraints weight = 4749.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123614 restraints weight = 3773.419| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13823 Z= 0.354 Angle : 0.839 15.701 18846 Z= 0.419 Chirality : 0.051 0.319 2187 Planarity : 0.005 0.049 2338 Dihedral : 7.562 89.580 2003 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.84 % Allowed : 13.64 % Favored : 83.52 % 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: -1.89 (0.20), residues: 1669 helix: 0.62 (0.21), residues: 580 sheet: -2.70 (0.24), residues: 383 loop : -1.93 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 138 TYR 0.024 0.002 TYR B 308 PHE 0.023 0.003 PHE A 55 TRP 0.019 0.002 TRP A 177 HIS 0.004 0.002 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00838 (13804) covalent geometry : angle 0.80574 (18799) SS BOND : bond 0.00543 ( 10) SS BOND : angle 1.60601 ( 20) hydrogen bonds : bond 0.04774 ( 666) hydrogen bonds : angle 5.23141 ( 2127) link_NAG-ASN : bond 0.00670 ( 9) link_NAG-ASN : angle 6.12555 ( 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 263 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7775 (t0) cc_final: 0.7483 (t0) REVERT: A 230 TYR cc_start: 0.8269 (m-80) cc_final: 0.7737 (m-80) REVERT: A 253 MET cc_start: 0.7298 (ptp) cc_final: 0.7024 (ptp) REVERT: B 32 ASP cc_start: 0.7632 (p0) cc_final: 0.7329 (p0) REVERT: B 93 ASP cc_start: 0.7495 (t0) cc_final: 0.7238 (t70) REVERT: B 234 MET cc_start: 0.7210 (mtt) cc_final: 0.6999 (mtt) REVERT: C 23 LYS cc_start: 0.8620 (tttt) cc_final: 0.7990 (tptt) REVERT: D 104 ASP cc_start: 0.8482 (t0) cc_final: 0.8250 (m-30) REVERT: D 240 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7630 (mp) REVERT: D 405 ILE cc_start: 0.7860 (tt) cc_final: 0.7489 (tp) REVERT: E 257 LEU cc_start: 0.8489 (tp) cc_final: 0.7822 (mp) outliers start: 41 outliers final: 29 residues processed: 250 average time/residue: 0.1079 time to fit residues: 40.2779 Evaluate side-chains 216 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 LEU 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 120 THR Chi-restraints excluded: chain C residue 140 THR 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 232 ILE 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 277 VAL 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: 3.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** 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 = 0.3668 r_free = 0.3668 target = 0.139421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121058 restraints weight = 20043.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124916 restraints weight = 10089.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127423 restraints weight = 6280.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129087 restraints weight = 4488.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130060 restraints weight = 3525.948| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13823 Z= 0.149 Angle : 0.665 13.704 18846 Z= 0.324 Chirality : 0.045 0.247 2187 Planarity : 0.004 0.048 2338 Dihedral : 6.846 81.793 2003 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.19 % Allowed : 16.55 % Favored : 80.26 % 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: -1.34 (0.21), residues: 1669 helix: 1.16 (0.22), residues: 583 sheet: -2.47 (0.25), residues: 363 loop : -1.70 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 190 TYR 0.030 0.002 TYR D 308 PHE 0.021 0.002 PHE C 406 TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00342 (13804) covalent geometry : angle 0.63122 (18799) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.52162 ( 20) hydrogen bonds : bond 0.03765 ( 666) hydrogen bonds : angle 4.72184 ( 2127) link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 5.41191 ( 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 257 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8279 (mtmm) REVERT: B 93 ASP cc_start: 0.7356 (t0) cc_final: 0.7149 (t70) REVERT: B 217 ILE cc_start: 0.8400 (mm) cc_final: 0.8164 (mt) REVERT: B 234 MET cc_start: 0.6942 (mtt) cc_final: 0.6728 (mtt) REVERT: C 23 LYS cc_start: 0.8533 (tttt) cc_final: 0.8002 (tptt) REVERT: C 278 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7305 (mtm180) REVERT: D 313 PHE cc_start: 0.7818 (t80) cc_final: 0.7377 (t80) REVERT: E 190 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6689 (mtt180) REVERT: E 266 PHE cc_start: 0.8292 (m-80) cc_final: 0.8073 (m-80) REVERT: E 300 LYS cc_start: 0.8434 (mttt) cc_final: 0.8129 (mttt) outliers start: 46 outliers final: 29 residues processed: 243 average time/residue: 0.1072 time to fit residues: 38.8898 Evaluate side-chains 221 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 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 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 B residue 284 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 120 THR 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 D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 SER 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 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124052 restraints weight = 20021.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127947 restraints weight = 10048.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130452 restraints weight = 6218.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132033 restraints weight = 4429.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133131 restraints weight = 3503.018| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13823 Z= 0.130 Angle : 0.635 12.906 18846 Z= 0.310 Chirality : 0.044 0.241 2187 Planarity : 0.004 0.044 2338 Dihedral : 6.521 76.662 2003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.12 % Allowed : 17.87 % Favored : 79.02 % 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: -0.95 (0.21), residues: 1669 helix: 1.47 (0.22), residues: 579 sheet: -2.13 (0.26), residues: 355 loop : -1.54 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.028 0.001 TYR D 308 PHE 0.019 0.001 PHE C 406 TRP 0.013 0.001 TRP E 471 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00283 (13804) covalent geometry : angle 0.60301 (18799) SS BOND : bond 0.00500 ( 10) SS BOND : angle 1.41858 ( 20) hydrogen bonds : bond 0.03404 ( 666) hydrogen bonds : angle 4.44693 ( 2127) link_NAG-ASN : bond 0.00981 ( 9) link_NAG-ASN : angle 5.15659 ( 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: 45 poor density : 210 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.7482 (m) cc_final: 0.7213 (t) REVERT: B 217 ILE cc_start: 0.8189 (mm) cc_final: 0.7983 (tt) REVERT: B 234 MET cc_start: 0.6838 (mtt) cc_final: 0.6635 (mtp) REVERT: C 23 LYS cc_start: 0.8541 (tttt) cc_final: 0.8007 (tptt) REVERT: C 25 MET cc_start: 0.8076 (ptp) cc_final: 0.7584 (ptt) REVERT: C 259 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7411 (mtp180) REVERT: C 270 MET cc_start: 0.8020 (mmm) cc_final: 0.6977 (mmt) REVERT: D 313 PHE cc_start: 0.7803 (t80) cc_final: 0.7386 (t80) REVERT: E 266 PHE cc_start: 0.8224 (m-80) cc_final: 0.7975 (m-80) REVERT: E 300 LYS cc_start: 0.8485 (mttt) cc_final: 0.8162 (mttt) outliers start: 45 outliers final: 32 residues processed: 233 average time/residue: 0.1024 time to fit residues: 36.2913 Evaluate side-chains 216 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 265 THR 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 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 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 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 SER 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 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 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: 5.9990 chunk 123 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** D 49 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.137110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119330 restraints weight = 20229.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123076 restraints weight = 10123.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125505 restraints weight = 6274.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127112 restraints weight = 4472.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128129 restraints weight = 3514.013| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13823 Z= 0.191 Angle : 0.682 13.340 18846 Z= 0.334 Chirality : 0.045 0.248 2187 Planarity : 0.004 0.044 2338 Dihedral : 6.583 72.611 2003 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.02 % Allowed : 19.18 % Favored : 76.80 % 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: -0.93 (0.21), residues: 1669 helix: 1.50 (0.22), residues: 579 sheet: -2.12 (0.25), residues: 400 loop : -1.46 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.026 0.002 TYR D 308 PHE 0.018 0.002 PHE C 406 TRP 0.015 0.001 TRP E 471 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00451 (13804) covalent geometry : angle 0.65001 (18799) SS BOND : bond 0.00415 ( 10) SS BOND : angle 1.85480 ( 20) hydrogen bonds : bond 0.03629 ( 666) hydrogen bonds : angle 4.57009 ( 2127) link_NAG-ASN : bond 0.00723 ( 9) link_NAG-ASN : angle 5.32210 ( 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 264 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7650 (t0) cc_final: 0.7389 (t0) REVERT: B 217 ILE cc_start: 0.8361 (mm) cc_final: 0.8093 (tt) REVERT: B 234 MET cc_start: 0.6973 (mtt) cc_final: 0.6746 (mtp) REVERT: C 23 LYS cc_start: 0.8570 (tttt) cc_final: 0.8006 (tptt) REVERT: D 313 PHE cc_start: 0.7851 (t80) cc_final: 0.7413 (t80) REVERT: D 405 ILE cc_start: 0.8010 (tt) cc_final: 0.7679 (tp) REVERT: E 32 ASN cc_start: 0.7969 (t0) cc_final: 0.7744 (t0) REVERT: E 114 LYS cc_start: 0.8636 (pttt) cc_final: 0.8200 (mmtt) REVERT: E 190 ARG cc_start: 0.7445 (ttm110) cc_final: 0.6677 (mtt180) REVERT: E 257 LEU cc_start: 0.8435 (tp) cc_final: 0.7816 (mp) REVERT: E 266 PHE cc_start: 0.8243 (m-80) cc_final: 0.7977 (m-80) outliers start: 58 outliers final: 46 residues processed: 245 average time/residue: 0.1047 time to fit residues: 39.2221 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 119 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 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 180 ASP 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 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 120 THR 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 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 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 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 154 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121570 restraints weight = 20077.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125424 restraints weight = 10079.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127892 restraints weight = 6233.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129544 restraints weight = 4436.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130620 restraints weight = 3480.045| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13823 Z= 0.147 Angle : 0.654 12.535 18846 Z= 0.320 Chirality : 0.044 0.273 2187 Planarity : 0.004 0.043 2338 Dihedral : 6.325 67.049 2003 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.39 % Allowed : 20.22 % Favored : 76.39 % 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: -0.83 (0.21), residues: 1669 helix: 1.54 (0.22), residues: 583 sheet: -2.09 (0.24), residues: 424 loop : -1.30 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.035 0.002 TYR D 308 PHE 0.018 0.001 PHE C 406 TRP 0.013 0.001 TRP E 471 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00339 (13804) covalent geometry : angle 0.62268 (18799) SS BOND : bond 0.00374 ( 10) SS BOND : angle 1.90641 ( 20) hydrogen bonds : bond 0.03419 ( 666) hydrogen bonds : angle 4.44598 ( 2127) link_NAG-ASN : bond 0.00727 ( 9) link_NAG-ASN : angle 5.08962 ( 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 256 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 THR cc_start: 0.8821 (t) cc_final: 0.8485 (m) REVERT: B 154 MET cc_start: 0.7709 (mpp) cc_final: 0.7455 (ptp) REVERT: B 234 MET cc_start: 0.6899 (mtt) cc_final: 0.6646 (mtp) REVERT: C 23 LYS cc_start: 0.8553 (tttt) cc_final: 0.7999 (tptt) REVERT: C 218 GLU cc_start: 0.7555 (tt0) cc_final: 0.7298 (tt0) REVERT: C 270 MET cc_start: 0.8110 (mmm) cc_final: 0.6922 (mmt) REVERT: D 313 PHE cc_start: 0.7822 (t80) cc_final: 0.7422 (t80) REVERT: E 32 ASN cc_start: 0.7910 (t0) cc_final: 0.7704 (t0) REVERT: E 114 LYS cc_start: 0.8606 (pttt) cc_final: 0.8238 (mmtt) REVERT: E 190 ARG cc_start: 0.7413 (ttm110) cc_final: 0.6664 (mtt180) REVERT: E 257 LEU cc_start: 0.8371 (tp) cc_final: 0.7770 (mp) REVERT: E 266 PHE cc_start: 0.8206 (m-80) cc_final: 0.7949 (m-80) REVERT: E 302 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8728 (t) outliers start: 49 outliers final: 40 residues processed: 240 average time/residue: 0.1028 time to fit residues: 37.7966 Evaluate side-chains 239 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 312 ASN 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 180 ASP 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 253 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL 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 D residue 61 THR 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 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 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 = 0.3640 r_free = 0.3640 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118688 restraints weight = 19767.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122539 restraints weight = 9592.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125025 restraints weight = 5823.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126647 restraints weight = 4094.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127712 restraints weight = 3195.548| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13823 Z= 0.153 Angle : 0.664 12.311 18846 Z= 0.323 Chirality : 0.045 0.274 2187 Planarity : 0.004 0.042 2338 Dihedral : 6.233 64.461 2003 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.46 % Allowed : 20.71 % Favored : 75.83 % 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: -0.80 (0.21), residues: 1669 helix: 1.53 (0.22), residues: 583 sheet: -2.03 (0.24), residues: 426 loop : -1.27 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.033 0.002 TYR D 308 PHE 0.017 0.001 PHE C 406 TRP 0.012 0.001 TRP D 250 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00353 (13804) covalent geometry : angle 0.63368 (18799) SS BOND : bond 0.00394 ( 10) SS BOND : angle 1.71842 ( 20) hydrogen bonds : bond 0.03420 ( 666) hydrogen bonds : angle 4.39795 ( 2127) link_NAG-ASN : bond 0.00671 ( 9) link_NAG-ASN : angle 5.06043 ( 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 258 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7741 (mp) cc_final: 0.7510 (mp) REVERT: B 120 THR cc_start: 0.8835 (t) cc_final: 0.8518 (m) REVERT: B 154 MET cc_start: 0.7697 (mpp) cc_final: 0.7450 (ptp) REVERT: B 234 MET cc_start: 0.6806 (mtt) cc_final: 0.6597 (mtp) REVERT: C 23 LYS cc_start: 0.8543 (tttt) cc_final: 0.7991 (tptt) REVERT: C 218 GLU cc_start: 0.7595 (tt0) cc_final: 0.7313 (tt0) REVERT: C 270 MET cc_start: 0.8190 (mmm) cc_final: 0.7554 (mmm) REVERT: D 240 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7345 (mp) REVERT: D 313 PHE cc_start: 0.7791 (t80) cc_final: 0.7378 (t80) REVERT: D 405 ILE cc_start: 0.8028 (tt) cc_final: 0.7692 (tp) REVERT: E 32 ASN cc_start: 0.7914 (t0) cc_final: 0.7616 (t0) REVERT: E 114 LYS cc_start: 0.8637 (pttt) cc_final: 0.8286 (mmtt) REVERT: E 190 ARG cc_start: 0.7382 (ttm110) cc_final: 0.6659 (mtt180) REVERT: E 257 LEU cc_start: 0.8387 (tp) cc_final: 0.7787 (mp) REVERT: E 266 PHE cc_start: 0.8207 (m-80) cc_final: 0.7924 (m-80) outliers start: 50 outliers final: 40 residues processed: 241 average time/residue: 0.1047 time to fit residues: 38.3140 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 312 ASN 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 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL 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 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 312 ASN 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 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119739 restraints weight = 20084.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123433 restraints weight = 9874.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125846 restraints weight = 6034.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127423 restraints weight = 4246.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128466 restraints weight = 3318.482| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13823 Z= 0.160 Angle : 0.667 12.111 18846 Z= 0.325 Chirality : 0.045 0.280 2187 Planarity : 0.004 0.042 2338 Dihedral : 6.225 61.017 2003 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.25 % Allowed : 20.71 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.75 (0.21), residues: 1669 helix: 1.54 (0.22), residues: 583 sheet: -1.97 (0.24), residues: 420 loop : -1.25 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.031 0.002 TYR D 308 PHE 0.017 0.001 PHE C 406 TRP 0.011 0.001 TRP D 250 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00374 (13804) covalent geometry : angle 0.63746 (18799) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.70001 ( 20) hydrogen bonds : bond 0.03439 ( 666) hydrogen bonds : angle 4.39249 ( 2127) link_NAG-ASN : bond 0.00649 ( 9) link_NAG-ASN : angle 5.01464 ( 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 267 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7681 (mp) cc_final: 0.7354 (mp) REVERT: A 270 MET cc_start: 0.7995 (tpp) cc_final: 0.7432 (mpp) REVERT: B 120 THR cc_start: 0.8838 (t) cc_final: 0.8544 (m) REVERT: B 154 MET cc_start: 0.7741 (mpp) cc_final: 0.7465 (ptp) REVERT: C 23 LYS cc_start: 0.8592 (tttt) cc_final: 0.8009 (tptt) REVERT: C 218 GLU cc_start: 0.7608 (tt0) cc_final: 0.7324 (tt0) REVERT: D 240 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7332 (mp) REVERT: D 313 PHE cc_start: 0.7822 (t80) cc_final: 0.7419 (t80) REVERT: D 405 ILE cc_start: 0.8060 (tt) cc_final: 0.7728 (tp) REVERT: E 32 ASN cc_start: 0.7921 (t0) cc_final: 0.7609 (t0) REVERT: E 114 LYS cc_start: 0.8611 (pttt) cc_final: 0.8312 (mmtt) REVERT: E 174 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6959 (mtp85) REVERT: E 190 ARG cc_start: 0.7414 (ttm110) cc_final: 0.6661 (mtt180) REVERT: E 257 LEU cc_start: 0.8379 (tp) cc_final: 0.7792 (mp) REVERT: E 266 PHE cc_start: 0.8186 (m-80) cc_final: 0.7913 (m-80) outliers start: 47 outliers final: 43 residues processed: 249 average time/residue: 0.1062 time to fit residues: 40.0381 Evaluate side-chains 255 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 312 ASN 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 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 120 THR 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 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 312 ASN 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 309 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: 3.9990 chunk 122 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 193 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121438 restraints weight = 20230.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125127 restraints weight = 10230.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127528 restraints weight = 6401.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129114 restraints weight = 4594.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130122 restraints weight = 3622.353| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13823 Z= 0.195 Angle : 0.695 12.126 18846 Z= 0.341 Chirality : 0.046 0.288 2187 Planarity : 0.004 0.042 2338 Dihedral : 6.343 59.364 2003 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.12 % Allowed : 21.33 % Favored : 75.55 % 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: -0.79 (0.21), residues: 1669 helix: 1.46 (0.22), residues: 583 sheet: -1.99 (0.24), residues: 420 loop : -1.23 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.031 0.002 TYR D 308 PHE 0.017 0.002 PHE C 406 TRP 0.012 0.001 TRP D 250 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00461 (13804) covalent geometry : angle 0.66644 (18799) SS BOND : bond 0.00391 ( 10) SS BOND : angle 1.72338 ( 20) hydrogen bonds : bond 0.03592 ( 666) hydrogen bonds : angle 4.47576 ( 2127) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 5.05231 ( 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 264 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7721 (mp) cc_final: 0.7348 (mp) REVERT: B 99 SER cc_start: 0.8904 (m) cc_final: 0.8476 (t) REVERT: B 120 THR cc_start: 0.8681 (t) cc_final: 0.8406 (m) REVERT: C 23 LYS cc_start: 0.8629 (tttt) cc_final: 0.7990 (tptt) REVERT: C 218 GLU cc_start: 0.7610 (tt0) cc_final: 0.7316 (tt0) REVERT: C 259 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7208 (mtm180) REVERT: C 270 MET cc_start: 0.8086 (mmm) cc_final: 0.7034 (mmt) REVERT: C 307 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 240 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7361 (mp) REVERT: D 313 PHE cc_start: 0.7842 (t80) cc_final: 0.7487 (t80) REVERT: D 405 ILE cc_start: 0.8146 (tt) cc_final: 0.7826 (tp) REVERT: E 114 LYS cc_start: 0.8628 (pttt) cc_final: 0.8336 (mmtt) REVERT: E 153 MET cc_start: 0.7448 (mtm) cc_final: 0.7225 (mtp) REVERT: E 190 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6683 (mtt180) REVERT: E 257 LEU cc_start: 0.8406 (tp) cc_final: 0.7808 (mp) REVERT: E 266 PHE cc_start: 0.8176 (m-80) cc_final: 0.7887 (m-80) outliers start: 45 outliers final: 41 residues processed: 246 average time/residue: 0.1053 time to fit residues: 38.9471 Evaluate side-chains 252 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 292 ILE 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 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 120 THR 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 268 LEU 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 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 309 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: 0.0370 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 overall best weight: 0.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 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 = 0.3780 r_free = 0.3780 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129964 restraints weight = 19473.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133537 restraints weight = 9924.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135849 restraints weight = 6230.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137371 restraints weight = 4486.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138359 restraints weight = 3543.619| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4315 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= 0.123 Angle : 0.654 10.513 18846 Z= 0.318 Chirality : 0.044 0.287 2187 Planarity : 0.004 0.041 2338 Dihedral : 6.053 57.969 2003 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.42 % Allowed : 22.02 % Favored : 75.55 % 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: -0.54 (0.21), residues: 1669 helix: 1.64 (0.22), residues: 583 sheet: -1.78 (0.25), residues: 414 loop : -1.11 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.030 0.001 TYR D 308 PHE 0.017 0.001 PHE C 406 TRP 0.011 0.001 TRP E 471 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00267 (13804) covalent geometry : angle 0.62845 (18799) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.55202 ( 20) hydrogen bonds : bond 0.03275 ( 666) hydrogen bonds : angle 4.28889 ( 2127) link_NAG-ASN : bond 0.00610 ( 9) link_NAG-ASN : angle 4.64827 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.35 seconds wall clock time: 34 minutes 50.32 seconds (2090.32 seconds total)