Starting phenix.real_space_refine on Fri Jul 3 10:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2026/7l31_23148.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 83 5.16 5 C 8883 2.51 5 N 2170 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13596 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2698 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2674 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2663 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2613 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'NAG': 2, 'SY9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.19 Number of scatterers: 13596 At special positions: 0 Unit cell: (91.3, 90.47, 128.65, 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 83 16.00 O 2460 8.00 N 2170 7.00 C 8883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " 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 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: 0.75 Conformation dependent library (CDL) restraints added in 496.9 milliseconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 23 sheets defined 36.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.811A pdb=" N ASP A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 96 through 100 removed outlier: 4.039A pdb=" N SER A 99 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 100 " --> pdb=" O LEU A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.705A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 281 Processing helix chain 'A' and resid 290 through 315 Processing helix chain 'A' and resid 384 through 416 Proline residue: A 400 - end of helix removed outlier: 3.599A pdb=" N ILE A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.828A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 288 through 315 removed outlier: 4.032A pdb=" N VAL B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 416 removed outlier: 3.585A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Proline residue: B 400 - end of helix removed outlier: 3.609A pdb=" N PHE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.649A pdb=" N MET C 154 " --> pdb=" O ASN C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 234 through 251 removed outlier: 3.798A pdb=" N SER C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 288 through 316 removed outlier: 3.633A pdb=" N ARG C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 412 Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 78 through 81 removed outlier: 3.832A pdb=" N ALA D 81 " --> pdb=" O SER D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.842A pdb=" N LEU D 97 " --> pdb=" O PRO D 94 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP D 98 " --> pdb=" O SER D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'D' and resid 151 through 154 removed outlier: 3.624A pdb=" N MET D 154 " --> pdb=" O ASN D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 234 through 251 removed outlier: 3.874A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 4.283A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 315 removed outlier: 3.849A pdb=" N TRP D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 415 Proline residue: D 400 - end of helix removed outlier: 4.163A pdb=" N THR D 413 " --> pdb=" O PHE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 92 through 95 removed outlier: 4.126A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 110 through 116 removed outlier: 3.525A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU E 116 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 275 through 294 removed outlier: 4.518A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 331 removed outlier: 3.815A pdb=" N VAL E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 474 removed outlier: 3.952A pdb=" N TYR E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 3.907A pdb=" N PHE E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.985A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.100A pdb=" N GLU A 110 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER A 144 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 184 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 5.999A pdb=" N THR A 215 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS A 216 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.613A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.661A pdb=" N ASP B 64 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 57 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 44 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLU B 176 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 46 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.661A pdb=" N ASP B 64 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 57 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLN B 184 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 50 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 105 through 107 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.552A pdb=" N LEU C 92 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 140 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 113 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 142 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.552A pdb=" N LEU C 92 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.184A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.332A pdb=" N GLU D 110 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER D 144 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 184 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB8, first strand: chain 'D' and resid 156 through 157 Processing sheet with id=AB9, first strand: chain 'D' and resid 207 through 209 removed outlier: 3.841A pdb=" N GLY D 212 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 105 through 108 removed outlier: 4.515A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 79 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 108 removed outlier: 4.515A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 79 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN E 200 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.572A pdb=" N ARG E 241 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AC5, first strand: chain 'E' and resid 223 through 224 752 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3463 1.33 - 1.46: 3094 1.46 - 1.58: 7274 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 13966 Sorted by residual: bond pdb=" N VAL D 58 " pdb=" CA VAL D 58 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.86e+00 bond pdb=" N GLY B 203 " pdb=" CA GLY B 203 " ideal model delta sigma weight residual 1.443 1.480 -0.037 1.17e-02 7.31e+03 9.85e+00 bond pdb=" C ALA A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 1.337 1.368 -0.032 1.06e-02 8.90e+03 8.88e+00 bond pdb=" N LYS B 207 " pdb=" CA LYS B 207 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.25e-02 6.40e+03 8.78e+00 bond pdb=" N ILE D 264 " pdb=" CA ILE D 264 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.34e+00 ... (remaining 13961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 18451 2.22 - 4.45: 476 4.45 - 6.67: 86 6.67 - 8.89: 29 8.89 - 11.12: 7 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C TYR C 235 " pdb=" N ILE C 236 " pdb=" CA ILE C 236 " ideal model delta sigma weight residual 120.24 123.39 -3.15 6.30e-01 2.52e+00 2.50e+01 angle pdb=" C TYR B 235 " pdb=" N ILE B 236 " pdb=" CA ILE B 236 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" N THR E 166 " pdb=" CA THR E 166 " pdb=" C THR E 166 " ideal model delta sigma weight residual 113.30 107.27 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" C VAL C 118 " pdb=" N THR C 119 " pdb=" CA THR C 119 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N ALA A 256 " pdb=" CA ALA A 256 " pdb=" C ALA A 256 " ideal model delta sigma weight residual 109.81 118.92 -9.11 2.21e+00 2.05e-01 1.70e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7244 17.74 - 35.48: 721 35.48 - 53.21: 125 53.21 - 70.95: 22 70.95 - 88.69: 7 Dihedral angle restraints: 8119 sinusoidal: 3134 harmonic: 4985 Sorted by residual: dihedral pdb=" CA CYS E 175 " pdb=" C CYS E 175 " pdb=" N LYS E 176 " pdb=" CA LYS E 176 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+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 -86.00 -39.07 -46.93 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA ILE A 69 " pdb=" C ILE A 69 " pdb=" N PHE A 70 " pdb=" CA PHE A 70 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 8116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1973 0.086 - 0.172: 198 0.172 - 0.259: 16 0.259 - 0.345: 13 0.345 - 0.431: 7 Chirality restraints: 2207 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 76 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" NAY SY9 A 503 " pdb=" CAS SY9 A 503 " pdb=" CAV SY9 A 503 " pdb=" CAX SY9 A 503 " both_signs ideal model delta sigma weight residual False -2.12 -2.54 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" NAY SY9 D 504 " pdb=" CAS SY9 D 504 " pdb=" CAV SY9 D 504 " pdb=" CAX SY9 D 504 " both_signs ideal model delta sigma weight residual False -2.12 -2.53 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 2204 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 45 " -0.006 2.00e-02 2.50e+03 2.50e-02 7.81e+00 pdb=" CG ASN C 45 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 45 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 45 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 193 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C GLN D 193 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN D 193 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE D 194 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 134 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C VAL E 134 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL E 134 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 135 " 0.015 2.00e-02 2.50e+03 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2374 2.77 - 3.30: 12355 3.30 - 3.83: 22064 3.83 - 4.37: 25066 4.37 - 4.90: 45072 Nonbonded interactions: 106931 Sorted by model distance: nonbonded pdb=" OG SER B 285 " pdb=" O GLN C 226 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 289 " pdb=" OH TYR A 410 " model vdw 2.233 3.040 nonbonded pdb=" O PHE B 409 " pdb=" OG1 THR B 413 " model vdw 2.242 3.040 nonbonded pdb=" O ASP B 121 " pdb=" OD1 ASP B 121 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR E 185 " pdb=" OD1 ASP E 187 " model vdw 2.252 3.040 ... (remaining 106926 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 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 21 or (resid 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 253 or (resid 254 through 2 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 257 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 315 or (resid 316 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 400 or (resid 401 through 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 408 or \ (resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 503)) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 21 or (resid 22 and (name N or name CA or na \ me C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 250 or (resid 251 and (name N or name CA or name C or name O or na \ me CB )) or resid 252 through 305 or (resid 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 315 or (resid 316 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 404 or (resid 405 and (name N or name CA or name C or name \ O or name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA o \ r name C or name O or name CB )) or resid 410 through 503)) selection = (chain 'C' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 21 or (resid 22 and (name N or name CA or name C or name \ O or name CB )) or resid 23 through 59 or (resid 60 and (name N or name CA or na \ me C or name O or name CB )) or resid 61 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 186 or (resid 1 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 386 or (resid 387 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 503)) selection = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 or (resid 253 through 256 and (name \ N or name CA or name C or name O or name CB )) or resid 257 through 400 or (resi \ d 401 through 402 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13981 Z= 0.264 Angle : 0.916 11.118 19088 Z= 0.475 Chirality : 0.061 0.431 2207 Planarity : 0.006 0.062 2345 Dihedral : 14.342 88.691 4867 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.28 % Allowed : 10.68 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.17), residues: 1666 helix: -1.41 (0.18), residues: 561 sheet: -3.12 (0.21), residues: 434 loop : -3.41 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 174 TYR 0.019 0.002 TYR E 303 PHE 0.025 0.002 PHE B 70 TRP 0.028 0.001 TRP B 293 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 (13966) covalent geometry : angle 0.90431 / 0.47 (19049) SS BOND : bond 0.00351 / 0.18 ( 6) SS BOND : angle 2.74365 / 1.91 ( 12) hydrogen bonds : bond 0.10608 / 6.82 ( 628) hydrogen bonds : angle 6.59789 / 4.43 ( 2193) link_NAG-ASN : bond 0.00535 / 0.33 ( 9) link_NAG-ASN : angle 3.66758 / 2.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 302 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8346 (tpp) cc_final: 0.8025 (mmm) REVERT: B 157 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8587 (mm-40) REVERT: B 227 MET cc_start: 0.7778 (ttp) cc_final: 0.7504 (ttp) REVERT: C 220 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8290 (mttp) REVERT: E 180 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 297 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6515 (mt-10) REVERT: E 319 PHE cc_start: 0.7743 (t80) cc_final: 0.7436 (m-10) outliers start: 4 outliers final: 3 residues processed: 306 average time/residue: 0.1050 time to fit residues: 46.3080 Evaluate side-chains 241 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN B 74 GLN B 233 GLN B 252 ASN C 68 ASN C 74 GLN C 116 HIS C 222 HIS D 38 ASN D 233 GLN D 312 ASN E 67 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106322 restraints weight = 19585.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109200 restraints weight = 12061.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111096 restraints weight = 8784.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112156 restraints weight = 7144.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113053 restraints weight = 6313.193| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13981 Z= 0.203 Angle : 0.703 10.481 19088 Z= 0.349 Chirality : 0.046 0.389 2207 Planarity : 0.005 0.051 2345 Dihedral : 5.623 59.599 1835 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.54 % Allowed : 17.20 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.19), residues: 1666 helix: 0.10 (0.21), residues: 566 sheet: -2.76 (0.21), residues: 433 loop : -3.06 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 278 TYR 0.017 0.002 TYR E 303 PHE 0.017 0.002 PHE B 70 TRP 0.023 0.001 TRP C 246 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (13966) covalent geometry : angle 0.69193 / 0.35 (19049) SS BOND : bond 0.00262 / 0.14 ( 6) SS BOND : angle 2.47923 / 1.81 ( 12) hydrogen bonds : bond 0.03578 / 2.39 ( 628) hydrogen bonds : angle 5.15116 / 3.46 ( 2193) link_NAG-ASN : bond 0.00319 / 0.20 ( 9) link_NAG-ASN : angle 3.05113 / 2.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.7507 (t0) cc_final: 0.7300 (t0) REVERT: C 96 MET cc_start: 0.7752 (ptp) cc_final: 0.7539 (ptp) REVERT: C 220 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8292 (mttp) REVERT: D 197 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8520 (mtmm) REVERT: D 253 MET cc_start: 0.6240 (pmm) cc_final: 0.5829 (pmm) REVERT: E 319 PHE cc_start: 0.7774 (t80) cc_final: 0.7477 (m-10) outliers start: 51 outliers final: 39 residues processed: 277 average time/residue: 0.0913 time to fit residues: 37.6569 Evaluate side-chains 260 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 116 optimal weight: 0.0670 chunk 62 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN A 252 ASN A 273 GLN D 233 GLN D 312 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106363 restraints weight = 19653.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109283 restraints weight = 12168.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111002 restraints weight = 8831.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112252 restraints weight = 7255.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113219 restraints weight = 6352.937| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13981 Z= 0.194 Angle : 0.687 10.125 19088 Z= 0.339 Chirality : 0.045 0.392 2207 Planarity : 0.005 0.047 2345 Dihedral : 5.520 56.794 1833 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.27 % Allowed : 19.49 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.20), residues: 1666 helix: 0.67 (0.22), residues: 566 sheet: -2.50 (0.22), residues: 429 loop : -2.83 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 80 TYR 0.022 0.002 TYR A 85 PHE 0.031 0.002 PHE D 249 TRP 0.025 0.001 TRP B 246 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (13966) covalent geometry : angle 0.67431 / 0.34 (19049) SS BOND : bond 0.00241 / 0.14 ( 6) SS BOND : angle 2.59316 / 1.84 ( 12) hydrogen bonds : bond 0.03393 / 2.25 ( 628) hydrogen bonds : angle 4.95981 / 3.31 ( 2193) link_NAG-ASN : bond 0.00405 / 0.28 ( 9) link_NAG-ASN : angle 3.15439 / 2.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 230 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8282 (t0) cc_final: 0.7985 (t0) REVERT: B 93 ASP cc_start: 0.7358 (t0) cc_final: 0.7156 (t0) REVERT: B 260 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.7017 (t) REVERT: C 96 MET cc_start: 0.7867 (ptp) cc_final: 0.7617 (ptp) REVERT: C 220 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8149 (mttp) REVERT: D 253 MET cc_start: 0.5828 (pmm) cc_final: 0.5609 (pmm) REVERT: E 319 PHE cc_start: 0.7806 (t80) cc_final: 0.7449 (m-10) outliers start: 76 outliers final: 51 residues processed: 278 average time/residue: 0.0851 time to fit residues: 36.4196 Evaluate side-chains 266 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 145 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 233 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104329 restraints weight = 19858.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107162 restraints weight = 12313.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109059 restraints weight = 8978.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110099 restraints weight = 7325.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110929 restraints weight = 6476.895| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13981 Z= 0.242 Angle : 0.717 10.090 19088 Z= 0.353 Chirality : 0.047 0.417 2207 Planarity : 0.005 0.051 2345 Dihedral : 5.564 55.197 1833 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.55 % Allowed : 20.87 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.20), residues: 1666 helix: 0.85 (0.22), residues: 566 sheet: -2.48 (0.23), residues: 429 loop : -2.70 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 278 TYR 0.018 0.002 TYR D 229 PHE 0.017 0.002 PHE E 69 TRP 0.030 0.001 TRP B 246 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (13966) covalent geometry : angle 0.70313 / 0.35 (19049) SS BOND : bond 0.00359 / 0.19 ( 6) SS BOND : angle 3.03091 / 2.13 ( 12) hydrogen bonds : bond 0.03572 / 2.38 ( 628) hydrogen bonds : angle 4.96892 / 3.31 ( 2193) link_NAG-ASN : bond 0.00337 / 0.21 ( 9) link_NAG-ASN : angle 3.25467 / 2.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 225 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.7051 (t) REVERT: C 96 MET cc_start: 0.7902 (ptp) cc_final: 0.7649 (ptp) REVERT: C 220 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8133 (mttp) REVERT: C 278 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7492 (mtt90) REVERT: D 233 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8408 (tp40) REVERT: D 253 MET cc_start: 0.5938 (pmm) cc_final: 0.5689 (pmm) outliers start: 80 outliers final: 63 residues processed: 279 average time/residue: 0.0821 time to fit residues: 35.6826 Evaluate side-chains 276 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 211 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 208 HIS A 273 GLN B 233 GLN C 233 GLN D 233 GLN D 312 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107186 restraints weight = 19723.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110142 restraints weight = 12133.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112116 restraints weight = 8779.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113234 restraints weight = 7096.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114176 restraints weight = 6231.608| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13981 Z= 0.146 Angle : 0.660 12.176 19088 Z= 0.323 Chirality : 0.045 0.295 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.375 58.918 1833 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.92 % Allowed : 23.16 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.20), residues: 1666 helix: 1.08 (0.22), residues: 566 sheet: -2.15 (0.23), residues: 414 loop : -2.64 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 278 TYR 0.022 0.001 TYR A 85 PHE 0.015 0.001 PHE E 319 TRP 0.028 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (13966) covalent geometry : angle 0.64091 / 0.32 (19049) SS BOND : bond 0.00218 / 0.11 ( 6) SS BOND : angle 2.51480 / 1.77 ( 12) hydrogen bonds : bond 0.03207 / 2.13 ( 628) hydrogen bonds : angle 4.70955 / 3.14 ( 2193) link_NAG-ASN : bond 0.00238 / 0.13 ( 9) link_NAG-ASN : angle 3.86827 / 2.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: A 407 ASN cc_start: 0.8217 (t0) cc_final: 0.7883 (t0) REVERT: B 260 VAL cc_start: 0.7240 (OUTLIER) cc_final: 0.7025 (t) REVERT: B 409 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7105 (t80) REVERT: C 154 MET cc_start: 0.7696 (mpp) cc_final: 0.7231 (ptp) REVERT: C 220 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8275 (mttp) REVERT: D 233 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7670 (tp-100) REVERT: D 253 MET cc_start: 0.5772 (pmm) cc_final: 0.5557 (pmm) outliers start: 71 outliers final: 49 residues processed: 282 average time/residue: 0.0851 time to fit residues: 37.0234 Evaluate side-chains 275 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN D 233 GLN D 312 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106989 restraints weight = 19618.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109966 restraints weight = 12130.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111689 restraints weight = 8793.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113070 restraints weight = 7230.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113744 restraints weight = 6314.477| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13981 Z= 0.148 Angle : 0.690 16.961 19088 Z= 0.335 Chirality : 0.045 0.289 2207 Planarity : 0.004 0.056 2345 Dihedral : 5.153 59.983 1832 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.99 % Allowed : 23.37 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1666 helix: 1.11 (0.22), residues: 566 sheet: -2.03 (0.23), residues: 418 loop : -2.56 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 278 TYR 0.016 0.001 TYR E 303 PHE 0.025 0.001 PHE B 302 TRP 0.028 0.001 TRP B 246 HIS 0.002 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13966) covalent geometry : angle 0.65697 / 0.33 (19049) SS BOND : bond 0.00208 / 0.11 ( 6) SS BOND : angle 4.14185 / 2.76 ( 12) hydrogen bonds : bond 0.03191 / 2.15 ( 628) hydrogen bonds : angle 4.66500 / 3.10 ( 2193) link_NAG-ASN : bond 0.00669 / 0.45 ( 9) link_NAG-ASN : angle 4.92332 / 3.24 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 0.495 Fit side-chains REVERT: A 407 ASN cc_start: 0.8203 (t0) cc_final: 0.7888 (t0) REVERT: B 260 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.7005 (t) REVERT: B 291 ASP cc_start: 0.8122 (m-30) cc_final: 0.7860 (m-30) REVERT: B 409 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7205 (t80) REVERT: C 233 GLN cc_start: 0.7706 (tt0) cc_final: 0.7456 (tt0) REVERT: D 233 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8065 (mm110) REVERT: D 240 LEU cc_start: 0.8113 (tp) cc_final: 0.7812 (tp) outliers start: 72 outliers final: 56 residues processed: 282 average time/residue: 0.0873 time to fit residues: 38.1808 Evaluate side-chains 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 233 GLN C 233 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107854 restraints weight = 19657.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110820 restraints weight = 12151.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112501 restraints weight = 8819.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113961 restraints weight = 7255.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114635 restraints weight = 6314.133| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13981 Z= 0.144 Angle : 0.665 10.030 19088 Z= 0.327 Chirality : 0.044 0.296 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.101 58.728 1832 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.85 % Allowed : 23.86 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1666 helix: 1.20 (0.22), residues: 566 sheet: -1.92 (0.24), residues: 418 loop : -2.49 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 278 TYR 0.022 0.001 TYR A 85 PHE 0.017 0.001 PHE E 319 TRP 0.030 0.001 TRP B 246 HIS 0.002 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13966) covalent geometry : angle 0.64601 / 0.32 (19049) SS BOND : bond 0.00167 / 0.09 ( 6) SS BOND : angle 3.42634 / 2.30 ( 12) hydrogen bonds : bond 0.03116 / 2.09 ( 628) hydrogen bonds : angle 4.58099 / 3.06 ( 2193) link_NAG-ASN : bond 0.00431 / 0.29 ( 9) link_NAG-ASN : angle 3.64543 / 2.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: A 407 ASN cc_start: 0.8193 (t0) cc_final: 0.7981 (t0) REVERT: B 260 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.7000 (t) REVERT: B 409 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 220 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8220 (mttp) REVERT: D 234 MET cc_start: 0.8338 (mmt) cc_final: 0.8133 (mmp) REVERT: E 180 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8141 (mt-10) outliers start: 70 outliers final: 57 residues processed: 280 average time/residue: 0.0829 time to fit residues: 36.3473 Evaluate side-chains 285 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 233 GLN C 233 GLN D 233 GLN D 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108291 restraints weight = 19572.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111198 restraints weight = 12046.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112871 restraints weight = 8769.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114245 restraints weight = 7220.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114958 restraints weight = 6309.995| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13981 Z= 0.153 Angle : 0.668 10.829 19088 Z= 0.326 Chirality : 0.046 0.577 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.116 58.532 1832 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.92 % Allowed : 24.83 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1666 helix: 1.21 (0.22), residues: 566 sheet: -1.86 (0.24), residues: 418 loop : -2.45 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 278 TYR 0.017 0.001 TYR E 303 PHE 0.013 0.001 PHE B 249 TRP 0.030 0.001 TRP B 246 HIS 0.003 0.001 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13966) covalent geometry : angle 0.64896 / 0.32 (19049) SS BOND : bond 0.00168 / 0.08 ( 6) SS BOND : angle 2.82484 / 1.92 ( 12) hydrogen bonds : bond 0.03119 / 2.07 ( 628) hydrogen bonds : angle 4.56344 / 3.05 ( 2193) link_NAG-ASN : bond 0.00408 / 0.27 ( 9) link_NAG-ASN : angle 3.82340 / 2.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8189 (t0) cc_final: 0.7975 (t0) REVERT: B 260 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6963 (t) REVERT: B 409 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7038 (t80) REVERT: C 220 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8137 (mttp) REVERT: C 233 GLN cc_start: 0.7695 (tt0) cc_final: 0.7302 (tt0) REVERT: D 240 LEU cc_start: 0.8059 (tp) cc_final: 0.7800 (tp) REVERT: E 180 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8176 (mt-10) outliers start: 71 outliers final: 63 residues processed: 275 average time/residue: 0.0886 time to fit residues: 37.3831 Evaluate side-chains 287 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 146 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109641 restraints weight = 19584.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112607 restraints weight = 11970.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114510 restraints weight = 8679.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115672 restraints weight = 7036.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116526 restraints weight = 6174.915| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13981 Z= 0.126 Angle : 0.699 25.087 19088 Z= 0.331 Chirality : 0.046 0.457 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.030 57.610 1832 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.72 % Allowed : 25.38 % Favored : 69.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.21), residues: 1666 helix: 1.33 (0.22), residues: 562 sheet: -1.73 (0.24), residues: 418 loop : -2.40 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.017 0.001 TYR E 303 PHE 0.013 0.001 PHE B 249 TRP 0.029 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13966) covalent geometry : angle 0.65645 / 0.32 (19049) SS BOND : bond 0.00153 / 0.07 ( 6) SS BOND : angle 2.63421 / 1.78 ( 12) hydrogen bonds : bond 0.03034 / 2.02 ( 628) hydrogen bonds : angle 4.48064 / 3.00 ( 2193) link_NAG-ASN : bond 0.00236 / 0.14 ( 9) link_NAG-ASN : angle 6.17870 / 4.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.9515 (t) cc_final: 0.9306 (t) REVERT: A 407 ASN cc_start: 0.8134 (t0) cc_final: 0.7889 (t0) REVERT: B 260 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6947 (t) REVERT: B 278 ARG cc_start: 0.7266 (mpp80) cc_final: 0.6143 (mpp80) REVERT: B 409 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6991 (t80) REVERT: C 220 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8247 (mttp) REVERT: C 233 GLN cc_start: 0.7580 (tt0) cc_final: 0.6955 (tt0) REVERT: D 240 LEU cc_start: 0.8000 (tp) cc_final: 0.7722 (tp) REVERT: E 190 ARG cc_start: 0.7386 (ttp80) cc_final: 0.7141 (ttp80) outliers start: 68 outliers final: 54 residues processed: 279 average time/residue: 0.0863 time to fit residues: 37.2695 Evaluate side-chains 281 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 0.0040 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 GLN C 226 GLN D 233 GLN D 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110691 restraints weight = 19430.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113797 restraints weight = 11566.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115840 restraints weight = 8218.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117059 restraints weight = 6579.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117969 restraints weight = 5736.896| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13981 Z= 0.114 Angle : 0.665 15.703 19088 Z= 0.320 Chirality : 0.044 0.372 2207 Planarity : 0.004 0.047 2345 Dihedral : 4.909 56.715 1832 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.74 % Allowed : 26.70 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1666 helix: 1.40 (0.22), residues: 562 sheet: -1.50 (0.25), residues: 418 loop : -2.34 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 278 TYR 0.019 0.001 TYR A 85 PHE 0.025 0.001 PHE B 20 TRP 0.035 0.001 TRP D 246 HIS 0.003 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13966) covalent geometry : angle 0.64260 / 0.31 (19049) SS BOND : bond 0.00152 / 0.07 ( 6) SS BOND : angle 2.53133 / 1.69 ( 12) hydrogen bonds : bond 0.02887 / 1.92 ( 628) hydrogen bonds : angle 4.38136 / 2.93 ( 2193) link_NAG-ASN : bond 0.00526 / 0.35 ( 9) link_NAG-ASN : angle 4.30435 / 3.03 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.9474 (t) cc_final: 0.9270 (t) REVERT: A 407 ASN cc_start: 0.8078 (t0) cc_final: 0.7825 (t0) REVERT: B 278 ARG cc_start: 0.7273 (mpp80) cc_final: 0.6440 (mpp80) REVERT: B 409 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 85 TYR cc_start: 0.6334 (t80) cc_final: 0.5967 (t80) REVERT: C 220 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8248 (mttp) REVERT: C 233 GLN cc_start: 0.7563 (tt0) cc_final: 0.6927 (tt0) REVERT: D 218 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: D 245 SER cc_start: 0.8642 (p) cc_final: 0.8339 (m) outliers start: 54 outliers final: 47 residues processed: 275 average time/residue: 0.0953 time to fit residues: 40.0374 Evaluate side-chains 267 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 34 optimal weight: 5.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN C 226 GLN D 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110863 restraints weight = 19523.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113847 restraints weight = 11841.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115787 restraints weight = 8483.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116855 restraints weight = 6864.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117676 restraints weight = 6046.787| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13981 Z= 0.131 Angle : 0.669 12.555 19088 Z= 0.322 Chirality : 0.044 0.348 2207 Planarity : 0.004 0.054 2345 Dihedral : 4.901 55.815 1832 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.95 % Allowed : 26.63 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1666 helix: 1.48 (0.22), residues: 562 sheet: -1.44 (0.25), residues: 418 loop : -2.30 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 278 TYR 0.017 0.001 TYR E 303 PHE 0.014 0.001 PHE B 20 TRP 0.039 0.001 TRP D 246 HIS 0.003 0.000 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (13966) covalent geometry : angle 0.65213 / 0.32 (19049) SS BOND : bond 0.00159 / 0.08 ( 6) SS BOND : angle 2.53671 / 1.70 ( 12) hydrogen bonds : bond 0.02937 / 1.96 ( 628) hydrogen bonds : angle 4.38118 / 2.93 ( 2193) link_NAG-ASN : bond 0.00474 / 0.31 ( 9) link_NAG-ASN : angle 3.65849 / 2.59 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.03 seconds wall clock time: 32 minutes 20.98 seconds (1940.98 seconds total)