Starting phenix.real_space_refine on Wed Mar 4 12:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l31_23148/03_2026/7l31_23148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l31_23148/03_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_23148/03_2026/7l31_23148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l31_23148/03_2026/7l31_23148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l31_23148/03_2026/7l31_23148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l31_23148/03_2026/7l31_23148.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.29, per 1000 atoms: 0.24 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: 1.07 Conformation dependent library (CDL) restraints added in 576.3 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: 0.40 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: 2.33 Time building geometry restraints manager: 1.45 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 - 20.66: 7892 20.66 - 41.32: 605 41.32 - 61.98: 92 61.98 - 82.64: 17 82.64 - 103.30: 7 Dihedral angle restraints: 8613 sinusoidal: 3628 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 8610 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 14.722 103.296 5361 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 covalent geometry : bond 0.00540 (13966) covalent geometry : angle 0.90431 (19049) SS BOND : bond 0.00351 ( 6) SS BOND : angle 2.74365 ( 12) hydrogen bonds : bond 0.10608 ( 628) hydrogen bonds : angle 6.59789 ( 2193) link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 3.66758 ( 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 : 0.508 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: 0.1226 time to fit residues: 53.9036 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 : 0.398 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3451 r_free = 0.3451 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106412 restraints weight = 19609.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109281 restraints weight = 12073.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111073 restraints weight = 8782.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112399 restraints weight = 7173.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113067 restraints weight = 6261.930| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13981 Z= 0.205 Angle : 0.709 10.519 19088 Z= 0.350 Chirality : 0.046 0.415 2207 Planarity : 0.005 0.051 2345 Dihedral : 7.549 62.635 2329 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.54 % Allowed : 17.13 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.87 (0.19), residues: 1666 helix: 0.12 (0.21), residues: 566 sheet: -2.75 (0.21), residues: 433 loop : -3.05 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 278 TYR 0.017 0.002 TYR E 230 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 covalent geometry : bond 0.00476 (13966) covalent geometry : angle 0.69682 (19049) SS BOND : bond 0.00527 ( 6) SS BOND : angle 2.41199 ( 12) hydrogen bonds : bond 0.03608 ( 628) hydrogen bonds : angle 5.13849 ( 2193) link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 3.13954 ( 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 : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.7453 (t0) cc_final: 0.7213 (t0) REVERT: C 96 MET cc_start: 0.7750 (ptp) cc_final: 0.7532 (ptp) REVERT: C 220 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8282 (mttp) REVERT: D 253 MET cc_start: 0.6250 (pmm) cc_final: 0.5839 (pmm) REVERT: E 319 PHE cc_start: 0.7772 (t80) cc_final: 0.7473 (m-10) outliers start: 51 outliers final: 39 residues processed: 277 average time/residue: 0.1113 time to fit residues: 45.5957 Evaluate side-chains 261 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 116 optimal weight: 0.0020 chunk 62 optimal weight: 8.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 252 ASN A 273 GLN B 53 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103105 restraints weight = 19936.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105901 restraints weight = 12373.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107775 restraints weight = 9047.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108781 restraints weight = 7386.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109622 restraints weight = 6542.087| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13981 Z= 0.309 Angle : 0.778 10.423 19088 Z= 0.384 Chirality : 0.049 0.371 2207 Planarity : 0.005 0.067 2345 Dihedral : 6.891 57.879 2327 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.89 % Allowed : 19.76 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.59 (0.20), residues: 1666 helix: 0.43 (0.21), residues: 566 sheet: -2.70 (0.22), residues: 431 loop : -2.88 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.021 0.002 TYR A 85 PHE 0.027 0.002 PHE D 249 TRP 0.027 0.002 TRP B 246 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00728 (13966) covalent geometry : angle 0.76254 (19049) SS BOND : bond 0.00186 ( 6) SS BOND : angle 2.91168 ( 12) hydrogen bonds : bond 0.03959 ( 628) hydrogen bonds : angle 5.20322 ( 2193) link_NAG-ASN : bond 0.00833 ( 9) link_NAG-ASN : angle 3.69767 ( 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: 85 poor density : 221 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: B 260 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7096 (t) REVERT: C 96 MET cc_start: 0.7908 (ptp) cc_final: 0.7630 (ptp) REVERT: C 220 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8162 (mttp) REVERT: D 253 MET cc_start: 0.6354 (pmm) cc_final: 0.6148 (pmm) REVERT: D 308 TYR cc_start: 0.7481 (t80) cc_final: 0.7237 (t80) outliers start: 85 outliers final: 59 residues processed: 278 average time/residue: 0.0956 time to fit residues: 41.1626 Evaluate side-chains 272 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 273 GLN 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 156 VAL 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 215 THR 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 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 64 ASP 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 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 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 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 145 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 252 ASN A 273 GLN B 233 GLN C 233 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106540 restraints weight = 19671.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109441 restraints weight = 12100.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111354 restraints weight = 8806.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112442 restraints weight = 7193.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113404 restraints weight = 6354.914| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13981 Z= 0.155 Angle : 0.664 10.232 19088 Z= 0.328 Chirality : 0.045 0.319 2207 Planarity : 0.005 0.055 2345 Dihedral : 6.339 58.430 2327 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.79 % Allowed : 22.12 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.20), residues: 1666 helix: 0.88 (0.22), residues: 566 sheet: -2.31 (0.23), residues: 414 loop : -2.76 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 278 TYR 0.017 0.001 TYR E 303 PHE 0.018 0.001 PHE E 319 TRP 0.026 0.001 TRP B 246 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00358 (13966) covalent geometry : angle 0.64993 (19049) SS BOND : bond 0.00319 ( 6) SS BOND : angle 2.86129 ( 12) hydrogen bonds : bond 0.03312 ( 628) hydrogen bonds : angle 4.86244 ( 2193) link_NAG-ASN : bond 0.00294 ( 9) link_NAG-ASN : angle 3.10492 ( 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 306 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8229 (t0) cc_final: 0.7888 (t0) REVERT: B 260 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.6993 (t) REVERT: C 220 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8229 (mttp) REVERT: D 233 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8327 (tp40) REVERT: D 253 MET cc_start: 0.6022 (pmm) cc_final: 0.5797 (pmm) outliers start: 69 outliers final: 49 residues processed: 278 average time/residue: 0.0993 time to fit residues: 42.5603 Evaluate side-chains 270 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL 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 189 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 270 MET 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 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 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 128 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108035 restraints weight = 19665.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111061 restraints weight = 12061.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113022 restraints weight = 8716.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114146 restraints weight = 7063.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115036 restraints weight = 6227.714| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13981 Z= 0.134 Angle : 0.668 13.417 19088 Z= 0.327 Chirality : 0.045 0.303 2207 Planarity : 0.004 0.052 2345 Dihedral : 6.101 58.852 2326 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.72 % Allowed : 23.72 % Favored : 71.57 % 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: -1.82 (0.20), residues: 1666 helix: 1.14 (0.22), residues: 562 sheet: -2.13 (0.23), residues: 418 loop : -2.62 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 278 TYR 0.023 0.001 TYR A 85 PHE 0.021 0.001 PHE A 302 TRP 0.028 0.001 TRP B 246 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00309 (13966) covalent geometry : angle 0.64679 (19049) SS BOND : bond 0.00202 ( 6) SS BOND : angle 3.81051 ( 12) hydrogen bonds : bond 0.03132 ( 628) hydrogen bonds : angle 4.65089 ( 2193) link_NAG-ASN : bond 0.00246 ( 9) link_NAG-ASN : angle 3.76621 ( 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 299 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 0.573 Fit side-chains REVERT: A 273 GLN cc_start: 0.7322 (tt0) cc_final: 0.7087 (tt0) REVERT: A 407 ASN cc_start: 0.8183 (t0) cc_final: 0.7857 (t0) REVERT: B 260 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.6977 (t) REVERT: B 291 ASP cc_start: 0.8096 (m-30) cc_final: 0.7811 (m-30) REVERT: B 409 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7093 (t80) REVERT: C 154 MET cc_start: 0.7610 (mpp) cc_final: 0.7135 (ptp) REVERT: C 233 GLN cc_start: 0.7681 (tt0) cc_final: 0.7352 (tt0) REVERT: C 278 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7205 (tpp80) REVERT: D 233 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8291 (mm-40) REVERT: D 253 MET cc_start: 0.5874 (pmm) cc_final: 0.5665 (pmm) outliers start: 68 outliers final: 53 residues processed: 278 average time/residue: 0.0992 time to fit residues: 42.5868 Evaluate side-chains 272 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASN 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 219 VAL 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 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 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 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 85 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3478 r_free = 0.3478 target = 0.132872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108415 restraints weight = 19653.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111400 restraints weight = 12066.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113335 restraints weight = 8739.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114417 restraints weight = 7096.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115233 restraints weight = 6257.080| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13981 Z= 0.130 Angle : 0.664 12.860 19088 Z= 0.323 Chirality : 0.046 0.447 2207 Planarity : 0.004 0.046 2345 Dihedral : 6.027 59.799 2326 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.85 % Allowed : 24.13 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1666 helix: 1.22 (0.22), residues: 562 sheet: -1.93 (0.23), residues: 418 loop : -2.55 (0.22), 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 0.021 0.001 PHE C 20 TRP 0.029 0.001 TRP B 246 HIS 0.002 0.000 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00298 (13966) covalent geometry : angle 0.64052 (19049) SS BOND : bond 0.00165 ( 6) SS BOND : angle 3.28634 ( 12) hydrogen bonds : bond 0.03095 ( 628) hydrogen bonds : angle 4.62371 ( 2193) link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 4.12118 ( 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 302 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 0.518 Fit side-chains REVERT: A 60 GLU cc_start: 0.7258 (mp0) cc_final: 0.7005 (mp0) REVERT: A 407 ASN cc_start: 0.8208 (t0) cc_final: 0.8001 (t0) REVERT: B 260 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6996 (t) REVERT: B 409 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7186 (t80) REVERT: C 278 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7328 (tpp80) REVERT: E 190 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7106 (ttp80) outliers start: 70 outliers final: 51 residues processed: 279 average time/residue: 0.1042 time to fit residues: 44.3764 Evaluate side-chains 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 85 LEU 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: 7.9990 chunk 161 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104780 restraints weight = 19769.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107792 restraints weight = 11958.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109595 restraints weight = 8567.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111074 restraints weight = 6968.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111809 restraints weight = 6037.950| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13981 Z= 0.193 Angle : 0.695 14.409 19088 Z= 0.337 Chirality : 0.046 0.295 2207 Planarity : 0.004 0.045 2345 Dihedral : 6.128 59.299 2326 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.79 % Allowed : 24.69 % Favored : 70.53 % 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: -1.67 (0.21), residues: 1666 helix: 1.17 (0.22), residues: 566 sheet: -2.03 (0.23), residues: 426 loop : -2.46 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.022 0.002 TYR A 85 PHE 0.017 0.001 PHE A 302 TRP 0.030 0.001 TRP B 246 HIS 0.003 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00452 (13966) covalent geometry : angle 0.66433 (19049) SS BOND : bond 0.00229 ( 6) SS BOND : angle 2.95539 ( 12) hydrogen bonds : bond 0.03264 ( 628) hydrogen bonds : angle 4.66340 ( 2193) link_NAG-ASN : bond 0.00278 ( 9) link_NAG-ASN : angle 5.13855 ( 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 300 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.528 Fit side-chains REVERT: A 407 ASN cc_start: 0.8222 (t0) cc_final: 0.8003 (t0) REVERT: B 227 MET cc_start: 0.7895 (ttm) cc_final: 0.7688 (ttp) REVERT: B 260 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6952 (t) REVERT: B 409 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 278 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7297 (tpp80) REVERT: D 234 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7327 (mmt) REVERT: D 240 LEU cc_start: 0.8150 (tp) cc_final: 0.7867 (tp) outliers start: 69 outliers final: 57 residues processed: 282 average time/residue: 0.1031 time to fit residues: 44.6046 Evaluate side-chains 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 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 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 231 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 VAL 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 234 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 0.0370 chunk 4 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 74 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 233 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 = 0.3460 r_free = 0.3460 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106888 restraints weight = 19530.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109832 restraints weight = 12104.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111757 restraints weight = 8792.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113009 restraints weight = 7141.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113676 restraints weight = 6252.385| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13981 Z= 0.159 Angle : 0.719 26.676 19088 Z= 0.340 Chirality : 0.047 0.536 2207 Planarity : 0.004 0.045 2345 Dihedral : 6.119 58.090 2326 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.13 % Allowed : 24.83 % Favored : 70.04 % 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: -1.52 (0.21), residues: 1666 helix: 1.29 (0.22), residues: 566 sheet: -1.86 (0.24), residues: 418 loop : -2.43 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.017 0.001 TYR E 303 PHE 0.021 0.001 PHE B 20 TRP 0.032 0.001 TRP B 246 HIS 0.003 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00366 (13966) covalent geometry : angle 0.65936 (19049) SS BOND : bond 0.00277 ( 6) SS BOND : angle 2.77559 ( 12) hydrogen bonds : bond 0.03159 ( 628) hydrogen bonds : angle 4.59314 ( 2193) link_NAG-ASN : bond 0.00543 ( 9) link_NAG-ASN : angle 7.44012 ( 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 303 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 229 time to evaluate : 0.487 Fit side-chains REVERT: A 407 ASN cc_start: 0.8195 (t0) cc_final: 0.7980 (t0) REVERT: B 260 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6943 (t) REVERT: B 278 ARG cc_start: 0.7213 (mtt90) cc_final: 0.6953 (mtt90) REVERT: B 409 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7080 (t80) REVERT: C 220 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8142 (mttp) REVERT: C 233 GLN cc_start: 0.7678 (tt0) cc_final: 0.7442 (tt0) REVERT: D 234 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7279 (mmt) REVERT: D 240 LEU cc_start: 0.8110 (tp) cc_final: 0.7810 (tp) REVERT: E 190 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7147 (ttp80) outliers start: 74 outliers final: 61 residues processed: 281 average time/residue: 0.1051 time to fit residues: 45.1758 Evaluate side-chains 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 169 THR Chi-restraints excluded: chain A residue 215 THR 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 205 CYS 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 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 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 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 234 MET 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: 0.9980 chunk 134 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 273 GLN B 233 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106836 restraints weight = 19594.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109965 restraints weight = 11720.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112022 restraints weight = 8334.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113225 restraints weight = 6684.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114117 restraints weight = 5843.251| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13981 Z= 0.127 Angle : 0.658 12.566 19088 Z= 0.319 Chirality : 0.045 0.471 2207 Planarity : 0.004 0.045 2345 Dihedral : 5.923 57.576 2326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.30 % Allowed : 25.73 % Favored : 69.97 % 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: -1.38 (0.21), residues: 1666 helix: 1.38 (0.22), residues: 562 sheet: -1.70 (0.24), residues: 418 loop : -2.37 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 278 TYR 0.021 0.001 TYR A 85 PHE 0.015 0.001 PHE C 175 TRP 0.038 0.001 TRP D 246 HIS 0.003 0.000 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00289 (13966) covalent geometry : angle 0.64001 (19049) SS BOND : bond 0.00161 ( 6) SS BOND : angle 2.58437 ( 12) hydrogen bonds : bond 0.03043 ( 628) hydrogen bonds : angle 4.48728 ( 2193) link_NAG-ASN : bond 0.00767 ( 9) link_NAG-ASN : angle 3.81935 ( 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 292 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.426 Fit side-chains REVERT: A 407 ASN cc_start: 0.8127 (t0) cc_final: 0.7913 (t0) REVERT: B 260 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6966 (t) REVERT: B 278 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6881 (mtt90) REVERT: B 409 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7027 (t80) REVERT: C 220 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8228 (mttp) REVERT: E 190 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7231 (ttp80) outliers start: 62 outliers final: 54 residues processed: 272 average time/residue: 0.1056 time to fit residues: 43.7687 Evaluate side-chains 276 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 215 THR 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 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 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 219 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 ILE 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 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 170 MET Chi-restraints excluded: chain D residue 202 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3436 r_free = 0.3436 target = 0.129524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104583 restraints weight = 19664.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107613 restraints weight = 11831.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109642 restraints weight = 8492.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110789 restraints weight = 6814.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111120 restraints weight = 5969.186| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13981 Z= 0.188 Angle : 0.712 18.502 19088 Z= 0.343 Chirality : 0.046 0.437 2207 Planarity : 0.004 0.044 2345 Dihedral : 6.014 57.583 2326 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.37 % Allowed : 25.80 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1666 helix: 1.32 (0.22), residues: 562 sheet: -1.75 (0.24), residues: 418 loop : -2.39 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 278 TYR 0.017 0.002 TYR E 303 PHE 0.020 0.001 PHE B 20 TRP 0.045 0.001 TRP D 246 HIS 0.003 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00443 (13966) covalent geometry : angle 0.68386 (19049) SS BOND : bond 0.00193 ( 6) SS BOND : angle 2.79903 ( 12) hydrogen bonds : bond 0.03207 ( 628) hydrogen bonds : angle 4.58138 ( 2193) link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 5.04092 ( 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 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8178 (t0) cc_final: 0.7948 (t0) REVERT: B 260 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.7053 (t) REVERT: B 409 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 220 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8228 (mttp) REVERT: D 218 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: D 240 LEU cc_start: 0.8125 (tp) cc_final: 0.7864 (tp) REVERT: E 190 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7164 (ttp80) outliers start: 63 outliers final: 57 residues processed: 262 average time/residue: 0.1059 time to fit residues: 42.5855 Evaluate side-chains 278 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 215 THR 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 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 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 45 ASN 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 219 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 ILE 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 160 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLU 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 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 285 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3440 r_free = 0.3440 target = 0.129835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104929 restraints weight = 19670.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107963 restraints weight = 11754.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109978 restraints weight = 8419.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111305 restraints weight = 6759.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112150 restraints weight = 5847.137| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13981 Z= 0.173 Angle : 0.689 14.181 19088 Z= 0.337 Chirality : 0.046 0.405 2207 Planarity : 0.004 0.045 2345 Dihedral : 6.058 57.879 2326 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.72 % Allowed : 25.87 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1666 helix: 1.35 (0.22), residues: 562 sheet: -1.73 (0.24), residues: 418 loop : -2.35 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.017 0.002 TYR E 303 PHE 0.018 0.001 PHE B 20 TRP 0.043 0.001 TRP D 246 HIS 0.003 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00406 (13966) covalent geometry : angle 0.66835 (19049) SS BOND : bond 0.00183 ( 6) SS BOND : angle 2.70556 ( 12) hydrogen bonds : bond 0.03191 ( 628) hydrogen bonds : angle 4.58351 ( 2193) link_NAG-ASN : bond 0.00401 ( 9) link_NAG-ASN : angle 4.17714 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.09 seconds wall clock time: 36 minutes 55.02 seconds (2215.02 seconds total)