Starting phenix.real_space_refine on Thu Jul 31 09:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkf_9403/07_2025/5bkf_9403.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, '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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, '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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6, '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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6, '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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} 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: 7.79, per 1000 atoms: 0.58 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: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.50 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: 3.99 Time building geometry restraints manager: 3.62 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 418 \ or resid 501 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 418 or \ resid 501 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 418 or resid 501 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP A 75 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 214 TYR 0.017 0.001 TYR C 308 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 9) link_NAG-ASN : angle 5.35454 ( 27) hydrogen bonds : bond 0.16505 ( 666) hydrogen bonds : angle 8.07071 ( 2127) SS BOND : bond 0.00282 ( 10) SS BOND : angle 1.43137 ( 20) covalent geometry : bond 0.00426 (13804) covalent geometry : angle 0.54132 (18799) *********************** 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 : 1.407 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: 0.7432 (pt0) cc_final: 0.6485 (pt0) REVERT: A 286 TYR cc_start: 0.8294 (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: 0.6879 (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: 0.8325 (tp40) cc_final: 0.7986 (tp40) outliers start: 5 outliers final: 1 residues processed: 276 average time/residue: 0.2845 time to fit residues: 112.7907 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 : 1.911 ------------------------------------------------------------------------------- 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 139 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 0.0010 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 312 ASN B 73 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125851 restraints weight = 19339.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129762 restraints weight = 9784.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132287 restraints weight = 6046.061| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13823 Z= 0.218 Angle : 0.737 14.529 18846 Z= 0.365 Chirality : 0.048 0.207 2187 Planarity : 0.005 0.049 2338 Dihedral : 7.856 87.712 2005 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.22 % Allowed : 9.70 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1669 helix: 0.91 (0.21), residues: 563 sheet: -3.05 (0.24), residues: 348 loop : -2.24 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.005 0.001 HIS E 132 PHE 0.020 0.002 PHE A 55 TYR 0.024 0.002 TYR B 308 ARG 0.007 0.001 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 9) link_NAG-ASN : angle 5.84830 ( 27) hydrogen bonds : bond 0.04186 ( 666) hydrogen bonds : angle 5.14165 ( 2127) SS BOND : bond 0.00769 ( 10) SS BOND : angle 2.07548 ( 20) covalent geometry : bond 0.00514 (13804) covalent geometry : angle 0.70061 (18799) *********************** 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 236 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8005 (mp10) cc_final: 0.7764 (mp10) REVERT: A 222 HIS cc_start: 0.7886 (m-70) cc_final: 0.7667 (m-70) REVERT: A 230 TYR cc_start: 0.8048 (m-80) cc_final: 0.7525 (m-80) REVERT: A 286 TYR cc_start: 0.8453 (p90) cc_final: 0.8249 (p90) REVERT: C 23 LYS cc_start: 0.8519 (tttt) cc_final: 0.7856 (tptt) REVERT: C 93 ASP cc_start: 0.7312 (t0) cc_final: 0.7106 (t70) REVERT: E 190 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6680 (mtt180) REVERT: E 300 LYS cc_start: 0.8424 (mttt) cc_final: 0.8143 (mttt) outliers start: 32 outliers final: 18 residues processed: 221 average time/residue: 0.2363 time to fit residues: 78.5555 Evaluate side-chains 191 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 239 LEU 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 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 192 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 312 ASN B 208 HIS D 157 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN 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 = 0.3712 r_free = 0.3712 target = 0.143128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125146 restraints weight = 19589.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129012 restraints weight = 9853.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131517 restraints weight = 6107.716| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13823 Z= 0.167 Angle : 0.667 13.849 18846 Z= 0.326 Chirality : 0.045 0.214 2187 Planarity : 0.004 0.045 2338 Dihedral : 6.701 85.898 2003 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.84 % Allowed : 12.67 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1669 helix: 1.21 (0.22), residues: 583 sheet: -2.65 (0.25), residues: 359 loop : -1.87 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 177 HIS 0.008 0.001 HIS B 208 PHE 0.018 0.002 PHE C 406 TYR 0.022 0.002 TYR C 308 ARG 0.005 0.000 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01138 ( 9) link_NAG-ASN : angle 5.50849 ( 27) hydrogen bonds : bond 0.03764 ( 666) hydrogen bonds : angle 4.74370 ( 2127) SS BOND : bond 0.00428 ( 10) SS BOND : angle 1.41751 ( 20) covalent geometry : bond 0.00388 (13804) covalent geometry : angle 0.63286 (18799) *********************** 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 251 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8283 (mtmm) REVERT: A 222 HIS cc_start: 0.8014 (m-70) cc_final: 0.7795 (m-70) REVERT: C 23 LYS cc_start: 0.8523 (tttt) cc_final: 0.7850 (tptt) REVERT: E 266 PHE cc_start: 0.8168 (m-80) cc_final: 0.7898 (m-80) REVERT: E 300 LYS cc_start: 0.8418 (mttt) cc_final: 0.8011 (mttt) outliers start: 41 outliers final: 23 residues processed: 235 average time/residue: 0.2327 time to fit residues: 81.8872 Evaluate side-chains 202 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP 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 292 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 153 MET 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 302 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.142742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125199 restraints weight = 19572.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129062 restraints weight = 9795.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131536 restraints weight = 6034.174| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13823 Z= 0.146 Angle : 0.640 13.211 18846 Z= 0.312 Chirality : 0.044 0.228 2187 Planarity : 0.004 0.045 2338 Dihedral : 6.427 80.299 2003 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.98 % Allowed : 14.68 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1669 helix: 1.69 (0.22), residues: 559 sheet: -2.33 (0.25), residues: 355 loop : -1.67 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 177 HIS 0.008 0.001 HIS B 208 PHE 0.018 0.001 PHE C 406 TYR 0.028 0.002 TYR E 325 ARG 0.009 0.001 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 9) link_NAG-ASN : angle 5.30520 ( 27) hydrogen bonds : bond 0.03528 ( 666) hydrogen bonds : angle 4.55752 ( 2127) SS BOND : bond 0.00402 ( 10) SS BOND : angle 1.37901 ( 20) covalent geometry : bond 0.00333 (13804) covalent geometry : angle 0.60677 (18799) *********************** 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 246 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8317 (mttm) REVERT: A 222 HIS cc_start: 0.8039 (m-70) cc_final: 0.7802 (m-70) REVERT: A 243 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7229 (mp) REVERT: B 217 ILE cc_start: 0.8305 (mm) cc_final: 0.8083 (mt) REVERT: C 23 LYS cc_start: 0.8543 (tttt) cc_final: 0.7979 (tptt) REVERT: E 190 ARG cc_start: 0.7364 (ttm110) cc_final: 0.6818 (mtt180) REVERT: E 266 PHE cc_start: 0.8221 (m-80) cc_final: 0.7985 (m-80) REVERT: E 300 LYS cc_start: 0.8410 (mttt) cc_final: 0.8017 (mttt) outliers start: 43 outliers final: 31 residues processed: 227 average time/residue: 0.2431 time to fit residues: 82.0139 Evaluate side-chains 215 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU 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 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain 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 39 PHE Chi-restraints excluded: chain D residue 61 THR 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 153 MET 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 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** 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 = 0.3711 r_free = 0.3711 target = 0.143100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125323 restraints weight = 19850.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129211 restraints weight = 9935.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131721 restraints weight = 6136.634| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13823 Z= 0.137 Angle : 0.629 12.803 18846 Z= 0.307 Chirality : 0.044 0.251 2187 Planarity : 0.004 0.043 2338 Dihedral : 6.310 75.152 2003 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.53 % Allowed : 16.14 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1669 helix: 1.83 (0.22), residues: 559 sheet: -2.06 (0.26), residues: 356 loop : -1.54 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 250 HIS 0.008 0.001 HIS B 208 PHE 0.017 0.001 PHE C 406 TYR 0.020 0.001 TYR B 308 ARG 0.008 0.001 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 9) link_NAG-ASN : angle 5.16593 ( 27) hydrogen bonds : bond 0.03369 ( 666) hydrogen bonds : angle 4.41826 ( 2127) SS BOND : bond 0.00373 ( 10) SS BOND : angle 1.37854 ( 20) covalent geometry : bond 0.00313 (13804) covalent geometry : angle 0.59679 (18799) *********************** 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 260 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.8072 (m-70) cc_final: 0.7796 (m-70) REVERT: A 243 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7212 (mp) REVERT: B 217 ILE cc_start: 0.8245 (mm) cc_final: 0.7990 (tt) REVERT: C 23 LYS cc_start: 0.8567 (tttt) cc_final: 0.7994 (tptt) REVERT: C 278 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7235 (mtm180) REVERT: D 313 PHE cc_start: 0.7791 (t80) cc_final: 0.7343 (t80) REVERT: E 190 ARG cc_start: 0.7336 (ttm110) cc_final: 0.6815 (mtt180) REVERT: E 266 PHE cc_start: 0.8219 (m-80) cc_final: 0.7975 (m-80) REVERT: E 300 LYS cc_start: 0.8416 (mttt) cc_final: 0.8023 (mttt) outliers start: 51 outliers final: 40 residues processed: 239 average time/residue: 0.3006 time to fit residues: 108.2968 Evaluate side-chains 228 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain 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 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 153 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** 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 = 0.3575 r_free = 0.3575 target = 0.131717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113587 restraints weight = 20681.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117375 restraints weight = 10119.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119829 restraints weight = 6222.724| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13823 Z= 0.297 Angle : 0.775 14.115 18846 Z= 0.383 Chirality : 0.048 0.259 2187 Planarity : 0.005 0.046 2338 Dihedral : 6.857 74.547 2003 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.95 % Allowed : 18.01 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1669 helix: 1.27 (0.22), residues: 579 sheet: -2.23 (0.26), residues: 347 loop : -1.74 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 177 HIS 0.004 0.001 HIS D 116 PHE 0.021 0.002 PHE A 55 TYR 0.024 0.002 TYR A 308 ARG 0.007 0.001 ARG E 241 Details of bonding type rmsd link_NAG-ASN : bond 0.01056 ( 9) link_NAG-ASN : angle 5.58404 ( 27) hydrogen bonds : bond 0.04230 ( 666) hydrogen bonds : angle 4.90154 ( 2127) SS BOND : bond 0.00487 ( 10) SS BOND : angle 1.52326 ( 20) covalent geometry : bond 0.00702 (13804) covalent geometry : angle 0.74471 (18799) *********************** 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 267 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7802 (t0) cc_final: 0.7501 (t0) REVERT: A 226 GLN cc_start: 0.8386 (pt0) cc_final: 0.8042 (pt0) REVERT: A 243 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7485 (mp) REVERT: B 120 THR cc_start: 0.8844 (t) cc_final: 0.8534 (m) REVERT: B 154 MET cc_start: 0.7518 (mpp) cc_final: 0.7291 (ptp) REVERT: B 217 ILE cc_start: 0.8525 (mm) cc_final: 0.8146 (tt) REVERT: C 23 LYS cc_start: 0.8643 (tttt) cc_final: 0.8010 (tptt) REVERT: C 270 MET cc_start: 0.8240 (mmm) cc_final: 0.7640 (mmm) REVERT: C 278 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: D 239 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8096 (tt) REVERT: D 313 PHE cc_start: 0.7962 (t80) cc_final: 0.7613 (t80) REVERT: D 405 ILE cc_start: 0.8110 (tt) cc_final: 0.7778 (tp) REVERT: E 114 LYS cc_start: 0.8664 (pttt) cc_final: 0.8232 (mmtt) REVERT: E 266 PHE cc_start: 0.8280 (m-80) cc_final: 0.8019 (m-80) REVERT: E 329 GLN cc_start: 0.8412 (tp40) cc_final: 0.7879 (tp40) outliers start: 57 outliers final: 43 residues processed: 248 average time/residue: 0.2332 time to fit residues: 87.0139 Evaluate side-chains 245 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain 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 239 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 67 ASN 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 208 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** 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 = 0.3594 r_free = 0.3594 target = 0.133052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115768 restraints weight = 20228.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119542 restraints weight = 9664.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121988 restraints weight = 5816.568| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13823 Z= 0.204 Angle : 0.709 13.379 18846 Z= 0.349 Chirality : 0.046 0.274 2187 Planarity : 0.004 0.046 2338 Dihedral : 6.684 70.844 2003 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.88 % Allowed : 19.53 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1669 helix: 1.36 (0.22), residues: 579 sheet: -2.15 (0.24), residues: 397 loop : -1.50 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.004 0.001 HIS A 222 PHE 0.019 0.002 PHE C 406 TYR 0.031 0.002 TYR D 308 ARG 0.009 0.001 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 9) link_NAG-ASN : angle 5.37013 ( 27) hydrogen bonds : bond 0.03788 ( 666) hydrogen bonds : angle 4.69882 ( 2127) SS BOND : bond 0.00481 ( 10) SS BOND : angle 2.08370 ( 20) covalent geometry : bond 0.00481 (13804) covalent geometry : angle 0.67710 (18799) *********************** 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 260 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7922 (mpp) cc_final: 0.7458 (mpp) REVERT: A 171 ASN cc_start: 0.7719 (t0) cc_final: 0.7447 (t0) REVERT: A 226 GLN cc_start: 0.8323 (pt0) cc_final: 0.8007 (pt0) REVERT: A 243 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7447 (mp) REVERT: B 120 THR cc_start: 0.8845 (t) cc_final: 0.8515 (m) REVERT: B 217 ILE cc_start: 0.8423 (mm) cc_final: 0.8161 (tt) REVERT: B 226 GLN cc_start: 0.8176 (pt0) cc_final: 0.7943 (pt0) REVERT: C 19 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6822 (t0) REVERT: C 23 LYS cc_start: 0.8598 (tttt) cc_final: 0.8009 (tptt) REVERT: C 278 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: D 313 PHE cc_start: 0.7926 (t80) cc_final: 0.7547 (t80) REVERT: D 405 ILE cc_start: 0.8127 (tt) cc_final: 0.7793 (tp) REVERT: E 114 LYS cc_start: 0.8617 (pttt) cc_final: 0.8235 (mmtt) REVERT: E 266 PHE cc_start: 0.8258 (m-80) cc_final: 0.7992 (m-80) REVERT: E 329 GLN cc_start: 0.8412 (tp40) cc_final: 0.8075 (tp40) outliers start: 56 outliers final: 40 residues processed: 241 average time/residue: 0.3146 time to fit residues: 114.4750 Evaluate side-chains 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain 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 292 ILE Chi-restraints excluded: chain D residue 409 PHE 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 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 Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122631 restraints weight = 20020.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126476 restraints weight = 9997.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128975 restraints weight = 6177.180| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13823 Z= 0.140 Angle : 0.654 12.304 18846 Z= 0.320 Chirality : 0.044 0.273 2187 Planarity : 0.004 0.045 2338 Dihedral : 6.359 68.554 2003 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.70 % Allowed : 20.71 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1669 helix: 1.57 (0.22), residues: 579 sheet: -2.02 (0.24), residues: 416 loop : -1.36 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 75 HIS 0.002 0.001 HIS A 222 PHE 0.019 0.001 PHE C 406 TYR 0.027 0.002 TYR D 308 ARG 0.009 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 9) link_NAG-ASN : angle 5.02616 ( 27) hydrogen bonds : bond 0.03410 ( 666) hydrogen bonds : angle 4.47678 ( 2127) SS BOND : bond 0.00391 ( 10) SS BOND : angle 1.79506 ( 20) covalent geometry : bond 0.00319 (13804) covalent geometry : angle 0.62418 (18799) *********************** 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 245 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7813 (mpp) cc_final: 0.7316 (mpp) REVERT: A 243 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7415 (mp) REVERT: B 120 THR cc_start: 0.8654 (t) cc_final: 0.8355 (m) REVERT: B 226 GLN cc_start: 0.8033 (pt0) cc_final: 0.7615 (pt0) REVERT: C 19 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6841 (t0) REVERT: C 23 LYS cc_start: 0.8607 (tttt) cc_final: 0.8032 (tptt) REVERT: C 270 MET cc_start: 0.8101 (mmm) cc_final: 0.7011 (mmt) REVERT: C 278 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7420 (mtm-85) REVERT: D 313 PHE cc_start: 0.7867 (t80) cc_final: 0.7494 (t80) REVERT: D 405 ILE cc_start: 0.8134 (tt) cc_final: 0.7811 (tp) REVERT: E 114 LYS cc_start: 0.8617 (pttt) cc_final: 0.8276 (mmtt) REVERT: E 174 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6872 (mtp85) REVERT: E 190 ARG cc_start: 0.7495 (ttm110) cc_final: 0.6814 (mtt180) REVERT: E 192 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 266 PHE cc_start: 0.8125 (m-80) cc_final: 0.7856 (m-80) REVERT: E 300 LYS cc_start: 0.8575 (mttt) cc_final: 0.8190 (mttt) REVERT: E 302 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8774 (t) outliers start: 39 outliers final: 28 residues processed: 231 average time/residue: 0.2409 time to fit residues: 83.2214 Evaluate side-chains 226 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 136 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124696 restraints weight = 19730.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128610 restraints weight = 9792.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131141 restraints weight = 6038.868| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13823 Z= 0.129 Angle : 0.648 11.346 18846 Z= 0.317 Chirality : 0.044 0.276 2187 Planarity : 0.004 0.044 2338 Dihedral : 6.189 65.701 2003 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.56 % Allowed : 21.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1669 helix: 1.68 (0.22), residues: 583 sheet: -1.83 (0.25), residues: 410 loop : -1.16 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 75 HIS 0.003 0.001 HIS A 222 PHE 0.018 0.001 PHE C 406 TYR 0.028 0.002 TYR D 308 ARG 0.008 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 9) link_NAG-ASN : angle 4.84869 ( 27) hydrogen bonds : bond 0.03286 ( 666) hydrogen bonds : angle 4.32851 ( 2127) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.61787 ( 20) covalent geometry : bond 0.00293 (13804) covalent geometry : angle 0.61981 (18799) *********************** 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 239 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.6972 (mmpt) cc_final: 0.6702 (mttm) REVERT: A 270 MET cc_start: 0.8005 (tpp) cc_final: 0.7506 (mpp) REVERT: B 120 THR cc_start: 0.8573 (t) cc_final: 0.8306 (m) REVERT: B 226 GLN cc_start: 0.8001 (pt0) cc_final: 0.7590 (pt0) REVERT: C 19 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6880 (t0) REVERT: C 23 LYS cc_start: 0.8566 (tttt) cc_final: 0.7990 (tptt) REVERT: C 270 MET cc_start: 0.8105 (mmm) cc_final: 0.7532 (mmm) REVERT: D 313 PHE cc_start: 0.7796 (t80) cc_final: 0.7407 (t80) REVERT: D 405 ILE cc_start: 0.8128 (tt) cc_final: 0.7795 (tp) REVERT: E 114 LYS cc_start: 0.8641 (pttt) cc_final: 0.8288 (mmtt) REVERT: E 190 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6861 (mtt180) REVERT: E 192 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 266 PHE cc_start: 0.8067 (m-80) cc_final: 0.7809 (m-80) outliers start: 37 outliers final: 30 residues processed: 227 average time/residue: 0.3195 time to fit residues: 111.9245 Evaluate side-chains 222 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 61 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 97 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121823 restraints weight = 19865.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125482 restraints weight = 9828.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127919 restraints weight = 6050.359| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13823 Z= 0.164 Angle : 0.699 16.670 18846 Z= 0.337 Chirality : 0.045 0.286 2187 Planarity : 0.004 0.045 2338 Dihedral : 6.291 67.135 2003 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.63 % Allowed : 21.68 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1669 helix: 1.62 (0.22), residues: 583 sheet: -1.87 (0.24), residues: 420 loop : -1.13 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 177 HIS 0.002 0.001 HIS A 222 PHE 0.019 0.002 PHE B 313 TYR 0.028 0.002 TYR D 308 ARG 0.007 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 9) link_NAG-ASN : angle 6.55912 ( 27) hydrogen bonds : bond 0.03469 ( 666) hydrogen bonds : angle 4.42233 ( 2127) SS BOND : bond 0.00386 ( 10) SS BOND : angle 1.66348 ( 20) covalent geometry : bond 0.00384 (13804) covalent geometry : angle 0.65168 (18799) ********************** 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 238 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.7717 (m) cc_final: 0.7291 (t) REVERT: A 40 LYS cc_start: 0.6978 (mmpt) cc_final: 0.6577 (mttm) REVERT: A 218 GLU cc_start: 0.7682 (pt0) cc_final: 0.7460 (pt0) REVERT: B 120 THR cc_start: 0.8653 (t) cc_final: 0.8374 (m) REVERT: B 226 GLN cc_start: 0.8035 (pt0) cc_final: 0.7589 (pt0) REVERT: C 19 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6874 (t0) REVERT: C 23 LYS cc_start: 0.8564 (tttt) cc_final: 0.7972 (tptt) REVERT: C 270 MET cc_start: 0.8277 (mmm) cc_final: 0.7619 (mmm) REVERT: C 307 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8575 (tm-30) REVERT: D 154 MET cc_start: 0.8623 (mpp) cc_final: 0.8357 (mpp) REVERT: D 313 PHE cc_start: 0.7831 (t80) cc_final: 0.7467 (t80) REVERT: D 405 ILE cc_start: 0.8152 (tt) cc_final: 0.7818 (tp) REVERT: E 114 LYS cc_start: 0.8648 (pttt) cc_final: 0.8341 (mmtt) REVERT: E 190 ARG cc_start: 0.7428 (ttm110) cc_final: 0.6811 (mtt180) REVERT: E 249 MET cc_start: 0.8378 (tmm) cc_final: 0.8153 (tmm) outliers start: 38 outliers final: 32 residues processed: 228 average time/residue: 0.2522 time to fit residues: 86.7162 Evaluate side-chains 233 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 61 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 281 LEU Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 110 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120498 restraints weight = 20313.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124230 restraints weight = 10189.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126677 restraints weight = 6339.795| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13823 Z= 0.183 Angle : 0.707 12.720 18846 Z= 0.345 Chirality : 0.046 0.285 2187 Planarity : 0.004 0.044 2338 Dihedral : 6.423 67.315 2003 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.49 % Allowed : 22.44 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1669 helix: 1.57 (0.22), residues: 583 sheet: -1.90 (0.24), residues: 420 loop : -1.12 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.003 0.001 HIS A 222 PHE 0.019 0.002 PHE C 313 TYR 0.027 0.002 TYR D 308 ARG 0.006 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 9) link_NAG-ASN : angle 5.85850 ( 27) hydrogen bonds : bond 0.03548 ( 666) hydrogen bonds : angle 4.50599 ( 2127) SS BOND : bond 0.00491 ( 10) SS BOND : angle 2.15139 ( 20) covalent geometry : bond 0.00431 (13804) covalent geometry : angle 0.66808 (18799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.48 seconds wall clock time: 74 minutes 15.71 seconds (4455.71 seconds total)