Starting phenix.real_space_refine on Wed Mar 4 12:53:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq8_33390/03_2026/7xq8_33390.map" } resolution = 3.3 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= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1587 atoms to isotropic. 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 42 5.16 5 C 7698 2.51 5 N 2251 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 12452 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 3979 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 40, 'TRANS': 554} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 884 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 8, 'ARG:plan': 13, 'TYR:plan': 7, 'PHE:plan': 8, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 368 Chain: "L" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1035 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 11, 'TRANS': 198} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 629 Unresolved non-hydrogen angles: 812 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 15, 'ARG:plan': 9, 'TYR:plan': 11, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'ASN:plan1': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 359 Chain: "v" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 3968 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 40, 'TRANS': 554} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 13, 'TYR:plan': 7, 'PHE:plan': 8, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 372 Chain: "R" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1035 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 11, 'TRANS': 198} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 629 Unresolved non-hydrogen angles: 812 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 15, 'ARG:plan': 9, 'TYR:plan': 11, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'ASN:plan1': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 359 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "B" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1131 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.14, per 1000 atoms: 0.25 Number of scatterers: 12452 At special positions: 0 Unit cell: (114.162, 140.01, 228.324, 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 42 16.00 O 2461 8.00 N 2251 7.00 C 7698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS v 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS v 257 " - pdb=" SG CYS v 320 " distance=1.95 Simple disulfide: pdb=" SG CYS v 367 " - pdb=" SG CYS v 426 " distance=2.03 Simple disulfide: pdb=" SG CYS v 474 " - pdb=" SG CYS v 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 122 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 63 " " NAG A 302 " - " ASN A 97 " " NAG A 303 " - " ASN A 57 " " NAG A 304 " - " ASN A 88 " " NAG A 305 " - " ASN A 112 " " NAG A 306 " - " ASN A 73 " " NAG B 301 " - " ASN B 101 " " NAG B 302 " - " ASN B 73 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 332 " " NAG C 603 " - " ASN C 402 " " NAG v 601 " - " ASN v 395 " " NAG v 602 " - " ASN v 402 " " NAG v 603 " - " ASN v 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 697.0 milliseconds 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3518 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 13.4% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.610A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.508A pdb=" N ASN C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 597 Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 187 through 191 removed outlier: 3.559A pdb=" N LYS L 190 " --> pdb=" O ASP L 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS L 191 " --> pdb=" O TYR L 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 187 through 191' Processing helix chain 'v' and resid 93 through 97 Processing helix chain 'v' and resid 198 through 204 Processing helix chain 'v' and resid 242 through 246 removed outlier: 4.097A pdb=" N PHE v 246 " --> pdb=" O ARG v 243 " (cutoff:3.500A) Processing helix chain 'v' and resid 309 through 314 Processing helix chain 'v' and resid 353 through 361 Processing helix chain 'v' and resid 414 through 420 Processing helix chain 'v' and resid 569 through 593 removed outlier: 4.221A pdb=" N THR v 589 " --> pdb=" O LEU v 585 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 129 Processing helix chain 'R' and resid 184 through 189 removed outlier: 4.037A pdb=" N GLU R 189 " --> pdb=" O LYS R 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.529A pdb=" N GLY A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.767A pdb=" N GLY A 101 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 171 Proline residue: A 159 - end of helix Processing helix chain 'B' and resid 68 through 72 removed outlier: 4.150A pdb=" N SER B 71 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.560A pdb=" N ASN B 117 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 180 Proline residue: B 176 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.801A pdb=" N GLY C 59 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG C 48 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP C 57 " --> pdb=" O ARG C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.146A pdb=" N LYS C 106 " --> pdb=" O PHE C 110D" (cutoff:3.500A) removed outlier: 8.258A pdb=" N PHE C 110D" --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.695A pdb=" N ASP C 155 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR C 188 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.695A pdb=" N ASP C 155 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR C 188 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 239 Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 239 Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 277 removed outlier: 3.551A pdb=" N GLN C 268 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 347 through 350 removed outlier: 5.283A pdb=" N LYS C 364 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 413 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 366 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA C 411 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU C 368 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 409 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 406 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 395 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.629A pdb=" N VAL C 390 " --> pdb=" O TRP C 382 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.534A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.707A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.306A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.306A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.751A pdb=" N ASN L 139 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU L 137 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER L 179 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 132 through 134 Processing sheet with id=AC2, first strand: chain 'L' and resid 155 through 156 Processing sheet with id=AC3, first strand: chain 'v' and resid 13 through 16 Processing sheet with id=AC4, first strand: chain 'v' and resid 20 through 22 removed outlier: 3.708A pdb=" N GLY v 59 " --> pdb=" O TRP v 46 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG v 48 " --> pdb=" O TRP v 57 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP v 57 " --> pdb=" O ARG v 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'v' and resid 20 through 22 removed outlier: 3.566A pdb=" N HIS v 112 " --> pdb=" O ARG v 104 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS v 106 " --> pdb=" O PHE v 110D" (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE v 110D" --> pdb=" O LYS v 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 130 through 135 removed outlier: 3.941A pdb=" N ASP v 155 " --> pdb=" O TYR v 188 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR v 188 " --> pdb=" O ASP v 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'v' and resid 130 through 135 removed outlier: 3.941A pdb=" N ASP v 155 " --> pdb=" O TYR v 188 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR v 188 " --> pdb=" O ASP v 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'v' and resid 162 through 166 Processing sheet with id=AC9, first strand: chain 'v' and resid 236 through 239 removed outlier: 3.506A pdb=" N ILE v 256 " --> pdb=" O PHE v 239 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE v 256 " --> pdb=" O LEU v 305 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU v 305 " --> pdb=" O ILE v 256 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN v 258 " --> pdb=" O SER v 303 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER v 303 " --> pdb=" O GLN v 258 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR v 260 " --> pdb=" O VAL v 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL v 301 " --> pdb=" O THR v 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'v' and resid 236 through 239 removed outlier: 3.506A pdb=" N ILE v 256 " --> pdb=" O PHE v 239 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE v 256 " --> pdb=" O LEU v 305 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU v 305 " --> pdb=" O ILE v 256 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN v 258 " --> pdb=" O SER v 303 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER v 303 " --> pdb=" O GLN v 258 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR v 260 " --> pdb=" O VAL v 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL v 301 " --> pdb=" O THR v 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'v' and resid 276 through 278 removed outlier: 3.937A pdb=" N TRP v 271 " --> pdb=" O VAL v 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL v 322 " --> pdb=" O PHE v 329 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'v' and resid 346 through 350 removed outlier: 4.084A pdb=" N THR v 363 " --> pdb=" O ILE v 413 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP v 371 " --> pdb=" O PHE v 405 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE v 405 " --> pdb=" O ASP v 371 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER v 406 " --> pdb=" O SER v 397 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU v 410 " --> pdb=" O HIS v 393 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'v' and resid 389 through 390 removed outlier: 4.323A pdb=" N TRP v 382 " --> pdb=" O VAL v 390 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'v' and resid 453 through 457 removed outlier: 3.690A pdb=" N THR v 473 " --> pdb=" O LEU v 457 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'v' and resid 453 through 457 removed outlier: 3.690A pdb=" N THR v 473 " --> pdb=" O LEU v 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'v' and resid 485 through 489 Processing sheet with id=AD8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.022A pdb=" N LEU R 11 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.022A pdb=" N LEU R 11 " --> pdb=" O GLN R 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 116 through 117 removed outlier: 3.588A pdb=" N ASN R 139 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN R 140 " --> pdb=" O TYR R 175 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR R 175 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 116 through 117 removed outlier: 3.588A pdb=" N ASN R 139 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN R 140 " --> pdb=" O TYR R 175 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR R 175 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 155 through 156 removed outlier: 3.574A pdb=" N CYS R 196 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS R 209 " --> pdb=" O CYS R 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.728A pdb=" N TYR A 104 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 103 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AE7, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.752A pdb=" N TRP B 47 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 52 through 53 652 hydrogen bonds defined for protein. 1620 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: 2.51 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2199 1.31 - 1.43: 3148 1.43 - 1.56: 7237 1.56 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 12643 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" CA PHE v 485 " pdb=" C PHE v 485 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.10e-02 8.26e+03 2.79e+01 bond pdb=" C PHE v 485 " pdb=" O PHE v 485 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.18e-02 7.18e+03 2.17e+01 bond pdb=" C VAL v 486 " pdb=" O VAL v 486 " ideal model delta sigma weight residual 1.238 1.181 0.056 1.28e-02 6.10e+03 1.94e+01 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 12638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 16948 2.23 - 4.46: 333 4.46 - 6.69: 41 6.69 - 8.92: 7 8.92 - 11.16: 5 Bond angle restraints: 17334 Sorted by residual: angle pdb=" N GLY v 531 " pdb=" CA GLY v 531 " pdb=" C GLY v 531 " ideal model delta sigma weight residual 114.61 125.59 -10.98 1.49e+00 4.50e-01 5.43e+01 angle pdb=" C PRO v 233 " pdb=" N PRO v 234 " pdb=" CA PRO v 234 " ideal model delta sigma weight residual 119.84 110.84 9.00 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 114.62 107.91 6.71 1.14e+00 7.69e-01 3.46e+01 angle pdb=" N LYS v 235 " pdb=" CA LYS v 235 " pdb=" C LYS v 235 " ideal model delta sigma weight residual 109.94 117.97 -8.03 1.57e+00 4.06e-01 2.61e+01 angle pdb=" C LEU A 134 " pdb=" N ASP A 135 " pdb=" CA ASP A 135 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 17329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 7331 24.55 - 49.11: 303 49.11 - 73.66: 34 73.66 - 98.21: 8 98.21 - 122.76: 9 Dihedral angle restraints: 7685 sinusoidal: 2263 harmonic: 5422 Sorted by residual: dihedral pdb=" CB CYS C 337 " pdb=" SG CYS C 337 " pdb=" SG CYS v 337 " pdb=" CB CYS v 337 " ideal model delta sinusoidal sigma weight residual 93.00 178.32 -85.32 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 126 " pdb=" CB CYS B 126 " ideal model delta sinusoidal sigma weight residual 93.00 160.31 -67.31 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CA SER C 263 " pdb=" C SER C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 7682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.121: 2133 1.121 - 2.243: 0 2.243 - 3.364: 0 3.364 - 4.486: 0 4.486 - 5.607: 1 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C1 NAG v 603 " pdb=" ND2 ASN v 332 " pdb=" C2 NAG v 603 " pdb=" O5 NAG v 603 " both_signs ideal model delta sigma weight residual False -2.40 3.21 -5.61 2.00e-01 2.50e+01 7.86e+02 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.95e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 395 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2131 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG v 603 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG v 603 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG v 603 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG v 603 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG v 603 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN v 332 " 0.049 2.00e-02 2.50e+03 5.88e-02 4.33e+01 pdb=" CG ASN v 332 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN v 332 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN v 332 " -0.104 2.00e-02 2.50e+03 pdb=" C1 NAG v 603 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN v 249 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO v 250 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO v 250 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO v 250 " -0.057 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 21 2.31 - 2.96: 5940 2.96 - 3.61: 16991 3.61 - 4.25: 24126 4.25 - 4.90: 41905 Nonbonded interactions: 88983 Sorted by model distance: nonbonded pdb=" CB PRO v 234 " pdb=" CZ PHE v 329 " model vdw 1.664 3.740 nonbonded pdb=" CB PRO v 233 " pdb=" CD1 PHE v 262 " model vdw 1.796 3.740 nonbonded pdb=" N PRO v 234 " pdb=" CE1 PHE v 262 " model vdw 2.092 3.420 nonbonded pdb=" O PRO v 234 " pdb=" CG PHE v 329 " model vdw 2.093 3.260 nonbonded pdb=" C PRO v 233 " pdb=" CE1 PHE v 262 " model vdw 2.107 3.570 ... (remaining 88978 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 'C' and ((resid 11 through 234 and (name N or name CA or name C or name O \ or name CB )) or resid 235 through 603)) selection = chain 'v' } ncs_group { reference = chain 'L' selection = chain 'R' } 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 individual isotropic 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 : 0.007 0.493 12669 Z= 0.342 Angle : 0.827 30.520 17398 Z= 0.451 Chirality : 0.132 5.607 2134 Planarity : 0.008 0.302 2315 Dihedral : 14.235 122.764 4134 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.50 % Favored : 92.91 % Rotamer: Outliers : 1.23 % Allowed : 0.89 % Favored : 97.88 % 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: -1.08 (0.20), residues: 1877 helix: 1.04 (0.37), residues: 203 sheet: -0.27 (0.19), residues: 767 loop : -1.52 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG v 251 TYR 0.010 0.001 TYR C 299 PHE 0.026 0.002 PHE v 485 TRP 0.019 0.002 TRP C 271 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00497 (12643) covalent geometry : angle 0.75695 (17334) SS BOND : bond 0.02515 ( 11) SS BOND : angle 2.75084 ( 22) hydrogen bonds : bond 0.23777 ( 571) hydrogen bonds : angle 9.35094 ( 1620) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.13195 ( 14) link_NAG-ASN : angle 6.56464 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: v 262 PHE cc_start: 0.2034 (OUTLIER) cc_final: 0.1518 (m-10) REVERT: B 155 ASN cc_start: 0.7259 (m110) cc_final: 0.6807 (m-40) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.1155 time to fit residues: 18.0404 Evaluate side-chains 87 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 235 LYS Chi-restraints excluded: chain v residue 262 PHE Chi-restraints excluded: chain v residue 263 SER Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 330 GLN Chi-restraints excluded: chain v residue 486 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 331 GLN v 393 HIS v 487 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.218428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175772 restraints weight = 19562.147| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.56 r_work: 0.3403 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.127 12669 Z= 0.462 Angle : 0.966 22.522 17398 Z= 0.485 Chirality : 0.066 1.540 2134 Planarity : 0.007 0.100 2315 Dihedral : 10.097 115.933 2264 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.57 % Favored : 91.80 % Rotamer: Outliers : 2.35 % Allowed : 11.62 % Favored : 86.03 % 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: -1.26 (0.19), residues: 1877 helix: 0.32 (0.36), residues: 206 sheet: -0.27 (0.19), residues: 764 loop : -1.60 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.018 0.003 TYR A 122 PHE 0.036 0.003 PHE v 479 TRP 0.020 0.003 TRP B 76 HIS 0.013 0.002 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.01115 (12643) covalent geometry : angle 0.92394 (17334) SS BOND : bond 0.01075 ( 11) SS BOND : angle 1.86047 ( 22) hydrogen bonds : bond 0.05095 ( 571) hydrogen bonds : angle 6.09904 ( 1620) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00933 ( 14) link_NAG-ASN : angle 5.68917 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 19 residues processed: 100 average time/residue: 0.1008 time to fit residues: 15.4012 Evaluate side-chains 98 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain v residue 235 LYS Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 160 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 393 HIS v 400 HIS ** v 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.222105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.179964 restraints weight = 19831.912| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.77 r_work: 0.3518 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12669 Z= 0.158 Angle : 0.691 17.966 17398 Z= 0.345 Chirality : 0.053 1.042 2134 Planarity : 0.005 0.099 2315 Dihedral : 8.797 114.048 2258 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.39 % Favored : 93.07 % Rotamer: Outliers : 2.12 % Allowed : 16.31 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1877 helix: 1.05 (0.37), residues: 206 sheet: -0.04 (0.19), residues: 756 loop : -1.39 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.011 0.001 TYR v 375 PHE 0.020 0.002 PHE C 479 TRP 0.015 0.001 TRP B 47 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00371 (12643) covalent geometry : angle 0.65151 (17334) SS BOND : bond 0.00335 ( 11) SS BOND : angle 1.11556 ( 22) hydrogen bonds : bond 0.03610 ( 571) hydrogen bonds : angle 5.16350 ( 1620) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00673 ( 14) link_NAG-ASN : angle 4.66635 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: v 271 TRP cc_start: 0.4621 (m100) cc_final: 0.4410 (m100) REVERT: v 317 MET cc_start: 0.8165 (mpt) cc_final: 0.7915 (mmp) REVERT: v 498 GLU cc_start: 0.8457 (pp20) cc_final: 0.8248 (pp20) REVERT: A 98 LYS cc_start: 0.8685 (tppt) cc_final: 0.8408 (tppt) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.1033 time to fit residues: 15.4731 Evaluate side-chains 91 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 50.0000 chunk 122 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS C 490 GLN ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 393 HIS A 117 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.221063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.179582 restraints weight = 19617.628| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.67 r_work: 0.3504 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12669 Z= 0.199 Angle : 0.691 14.825 17398 Z= 0.347 Chirality : 0.051 0.684 2134 Planarity : 0.005 0.098 2315 Dihedral : 8.472 115.917 2251 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.82 % Favored : 92.65 % Rotamer: Outliers : 3.24 % Allowed : 17.99 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1877 helix: 1.17 (0.37), residues: 206 sheet: 0.06 (0.19), residues: 758 loop : -1.30 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.012 0.002 TYR v 375 PHE 0.020 0.002 PHE v 479 TRP 0.013 0.001 TRP B 47 HIS 0.017 0.002 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00476 (12643) covalent geometry : angle 0.65881 (17334) SS BOND : bond 0.00394 ( 11) SS BOND : angle 1.23830 ( 22) hydrogen bonds : bond 0.03529 ( 571) hydrogen bonds : angle 4.81469 ( 1620) Misc. bond : bond 0.00021 ( 1) link_NAG-ASN : bond 0.00645 ( 14) link_NAG-ASN : angle 4.19294 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: v 247 PHE cc_start: 0.7471 (p90) cc_final: 0.7234 (p90) REVERT: v 315 GLN cc_start: 0.7459 (mp10) cc_final: 0.7123 (mp10) REVERT: v 317 MET cc_start: 0.8172 (mpt) cc_final: 0.7858 (mmp) REVERT: v 498 GLU cc_start: 0.8489 (pp20) cc_final: 0.8257 (pp20) REVERT: v 564 GLU cc_start: 0.8095 (pt0) cc_final: 0.7856 (pt0) REVERT: A 98 LYS cc_start: 0.8701 (tppt) cc_final: 0.8463 (tppt) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.0926 time to fit residues: 15.2096 Evaluate side-chains 96 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 520 ILE Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 65 optimal weight: 50.0000 chunk 155 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 70.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 116 optimal weight: 0.0870 chunk 112 optimal weight: 7.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 393 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.218486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.168927 restraints weight = 19597.687| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.54 r_work: 0.3380 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 12669 Z= 0.381 Angle : 0.828 13.675 17398 Z= 0.417 Chirality : 0.055 0.583 2134 Planarity : 0.006 0.096 2315 Dihedral : 8.658 118.412 2250 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.51 % Favored : 91.85 % Rotamer: Outliers : 4.69 % Allowed : 19.11 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1877 helix: 0.56 (0.36), residues: 206 sheet: 0.09 (0.19), residues: 752 loop : -1.44 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.016 0.002 TYR v 500 PHE 0.030 0.003 PHE v 479 TRP 0.019 0.002 TRP B 76 HIS 0.013 0.002 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00919 (12643) covalent geometry : angle 0.79990 (17334) SS BOND : bond 0.00764 ( 11) SS BOND : angle 1.57000 ( 22) hydrogen bonds : bond 0.04248 ( 571) hydrogen bonds : angle 4.94803 ( 1620) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00527 ( 14) link_NAG-ASN : angle 4.32554 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: C 271 TRP cc_start: 0.7590 (m100) cc_final: 0.7370 (m100) REVERT: v 247 PHE cc_start: 0.7573 (p90) cc_final: 0.7293 (p90) REVERT: v 313 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.7004 (mm) REVERT: v 315 GLN cc_start: 0.7705 (mp10) cc_final: 0.7288 (mp10) REVERT: v 317 MET cc_start: 0.8090 (mpt) cc_final: 0.7602 (mmp) REVERT: v 498 GLU cc_start: 0.8500 (pp20) cc_final: 0.8170 (pp20) REVERT: v 564 GLU cc_start: 0.8209 (pt0) cc_final: 0.7964 (pt0) REVERT: A 98 LYS cc_start: 0.8750 (tppt) cc_final: 0.8480 (tppt) outliers start: 42 outliers final: 34 residues processed: 118 average time/residue: 0.0855 time to fit residues: 16.2935 Evaluate side-chains 114 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 313 LEU Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 379 THR Chi-restraints excluded: chain v residue 453 ASP Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 520 ILE Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 20 optimal weight: 50.0000 chunk 125 optimal weight: 0.5980 chunk 7 optimal weight: 50.0000 chunk 70 optimal weight: 0.0050 chunk 158 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 119 optimal weight: 0.0670 chunk 126 optimal weight: 0.5980 chunk 18 optimal weight: 50.0000 overall best weight: 0.6534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.222742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.174545 restraints weight = 19633.566| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.64 r_work: 0.3525 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12669 Z= 0.138 Angle : 0.658 11.922 17398 Z= 0.327 Chirality : 0.048 0.493 2134 Planarity : 0.004 0.057 2315 Dihedral : 7.976 115.526 2250 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.45 % Favored : 93.07 % Rotamer: Outliers : 3.24 % Allowed : 20.45 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1877 helix: 1.08 (0.37), residues: 212 sheet: 0.22 (0.19), residues: 755 loop : -1.22 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG v 243 TYR 0.012 0.001 TYR v 375 PHE 0.020 0.001 PHE v 246 TRP 0.015 0.001 TRP B 47 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00320 (12643) covalent geometry : angle 0.62953 (17334) SS BOND : bond 0.00483 ( 11) SS BOND : angle 0.95275 ( 22) hydrogen bonds : bond 0.03133 ( 571) hydrogen bonds : angle 4.47886 ( 1620) Misc. bond : bond 0.00015 ( 1) link_NAG-ASN : bond 0.00635 ( 14) link_NAG-ASN : angle 3.89599 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.447 Fit side-chains REVERT: C 353 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6777 (p) REVERT: v 247 PHE cc_start: 0.7606 (p90) cc_final: 0.7386 (p90) REVERT: v 313 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6707 (mm) REVERT: v 315 GLN cc_start: 0.7550 (mp10) cc_final: 0.7095 (mp10) REVERT: v 317 MET cc_start: 0.8058 (mpt) cc_final: 0.7569 (mmp) REVERT: v 498 GLU cc_start: 0.8320 (pp20) cc_final: 0.8054 (pp20) REVERT: A 98 LYS cc_start: 0.8698 (tppt) cc_final: 0.8484 (tppt) REVERT: B 110 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8382 (mp10) outliers start: 29 outliers final: 20 residues processed: 108 average time/residue: 0.0805 time to fit residues: 14.4531 Evaluate side-chains 102 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 313 LEU Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 28 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 40.0000 chunk 148 optimal weight: 120.0000 chunk 121 optimal weight: 1.9990 chunk 158 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** v 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 277 GLN ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 315 GLN v 386 ASN v 393 HIS ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.211465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169833 restraints weight = 19406.826| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.39 r_work: 0.3321 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.253 12669 Z= 1.134 Angle : 1.495 24.151 17398 Z= 0.759 Chirality : 0.090 0.646 2134 Planarity : 0.010 0.110 2315 Dihedral : 9.901 121.451 2250 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.48 % Favored : 89.66 % Rotamer: Outliers : 7.15 % Allowed : 19.44 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.23 % 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: -1.69 (0.19), residues: 1877 helix: -1.55 (0.30), residues: 219 sheet: -0.23 (0.19), residues: 757 loop : -1.78 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 45 TYR 0.031 0.006 TYR C 500 PHE 0.080 0.007 PHE v 479 TRP 0.053 0.007 TRP B 76 HIS 0.028 0.005 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.02729 (12643) covalent geometry : angle 1.47216 (17334) SS BOND : bond 0.01793 ( 11) SS BOND : angle 2.66063 ( 22) hydrogen bonds : bond 0.07401 ( 571) hydrogen bonds : angle 5.83111 ( 1620) Misc. bond : bond 0.00043 ( 1) link_NAG-ASN : bond 0.00835 ( 14) link_NAG-ASN : angle 5.25243 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 74 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: C 299 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: C 593 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7908 (mm) REVERT: v 247 PHE cc_start: 0.7725 (p90) cc_final: 0.7440 (p90) REVERT: v 564 GLU cc_start: 0.8564 (pt0) cc_final: 0.8317 (pt0) outliers start: 64 outliers final: 47 residues processed: 125 average time/residue: 0.0852 time to fit residues: 17.3665 Evaluate side-chains 120 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 71 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 379 THR Chi-restraints excluded: chain v residue 453 ASP Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 541 GLU Chi-restraints excluded: chain v residue 553 ASP Chi-restraints excluded: chain v residue 573 THR Chi-restraints excluded: chain v residue 579 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 100 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 62 optimal weight: 120.0000 chunk 132 optimal weight: 0.6980 chunk 11 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.219314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169267 restraints weight = 19656.268| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.64 r_work: 0.3422 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 0.052 12669 Z= 0.187 Angle : 0.747 11.866 17398 Z= 0.369 Chirality : 0.051 0.464 2134 Planarity : 0.005 0.066 2315 Dihedral : 8.404 117.108 2250 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.82 % Favored : 92.59 % Rotamer: Outliers : 3.46 % Allowed : 23.35 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1877 helix: 0.29 (0.35), residues: 212 sheet: 0.10 (0.20), residues: 745 loop : -1.44 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 423 TYR 0.015 0.001 TYR v 375 PHE 0.022 0.002 PHE C 479 TRP 0.029 0.002 TRP C 271 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00442 (12643) covalent geometry : angle 0.71198 (17334) SS BOND : bond 0.00327 ( 11) SS BOND : angle 1.07660 ( 22) hydrogen bonds : bond 0.03566 ( 571) hydrogen bonds : angle 4.71378 ( 1620) Misc. bond : bond 0.00030 ( 1) link_NAG-ASN : bond 0.00654 ( 14) link_NAG-ASN : angle 4.63141 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.488 Fit side-chains REVERT: v 247 PHE cc_start: 0.7759 (p90) cc_final: 0.7405 (p90) REVERT: v 315 GLN cc_start: 0.7638 (mp10) cc_final: 0.7333 (mp10) REVERT: v 498 GLU cc_start: 0.8464 (pp20) cc_final: 0.7779 (pp20) REVERT: v 564 GLU cc_start: 0.8265 (pt0) cc_final: 0.7994 (pt0) REVERT: B 83 ASP cc_start: 0.6619 (p0) cc_final: 0.6414 (p0) REVERT: B 110 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8201 (mp10) outliers start: 31 outliers final: 21 residues processed: 104 average time/residue: 0.0922 time to fit residues: 15.3743 Evaluate side-chains 100 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 93 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 125 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 chunk 80 optimal weight: 100.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.218962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.176415 restraints weight = 19443.853| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.61 r_work: 0.3416 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12669 Z= 0.260 Angle : 0.769 12.608 17398 Z= 0.381 Chirality : 0.052 0.437 2134 Planarity : 0.006 0.097 2315 Dihedral : 8.309 117.867 2250 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.30 % Favored : 92.12 % Rotamer: Outliers : 3.91 % Allowed : 22.68 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1877 helix: 0.34 (0.36), residues: 218 sheet: 0.11 (0.20), residues: 759 loop : -1.31 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 423 TYR 0.015 0.002 TYR v 375 PHE 0.023 0.002 PHE C 479 TRP 0.021 0.002 TRP C 271 HIS 0.010 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00627 (12643) covalent geometry : angle 0.73927 (17334) SS BOND : bond 0.00524 ( 11) SS BOND : angle 1.32864 ( 22) hydrogen bonds : bond 0.03756 ( 571) hydrogen bonds : angle 4.65374 ( 1620) Misc. bond : bond 0.00035 ( 1) link_NAG-ASN : bond 0.00561 ( 14) link_NAG-ASN : angle 4.26948 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.442 Fit side-chains REVERT: v 247 PHE cc_start: 0.7659 (p90) cc_final: 0.7366 (p90) REVERT: v 315 GLN cc_start: 0.7158 (mp10) cc_final: 0.6859 (mp10) REVERT: v 498 GLU cc_start: 0.8596 (pp20) cc_final: 0.7974 (pp20) REVERT: v 564 GLU cc_start: 0.8326 (pt0) cc_final: 0.8058 (pt0) REVERT: B 83 ASP cc_start: 0.6875 (p0) cc_final: 0.6434 (p0) REVERT: B 87 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8352 (tp-100) outliers start: 35 outliers final: 30 residues processed: 109 average time/residue: 0.0931 time to fit residues: 16.0256 Evaluate side-chains 108 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 320.0000 chunk 99 optimal weight: 30.0000 chunk 60 optimal weight: 50.0000 chunk 170 optimal weight: 0.6980 chunk 101 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.214746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162980 restraints weight = 19513.328| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.65 r_work: 0.3312 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.143 12669 Z= 0.547 Angle : 0.994 20.554 17398 Z= 0.499 Chirality : 0.061 0.419 2134 Planarity : 0.007 0.092 2315 Dihedral : 8.844 119.456 2250 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.58 % Favored : 90.78 % Rotamer: Outliers : 4.25 % Allowed : 22.68 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.14 (0.20), residues: 1877 helix: -0.27 (0.34), residues: 212 sheet: -0.02 (0.20), residues: 759 loop : -1.52 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 126 TYR 0.020 0.003 TYR v 500 PHE 0.043 0.004 PHE v 479 TRP 0.027 0.003 TRP B 76 HIS 0.017 0.003 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.01324 (12643) covalent geometry : angle 0.96840 (17334) SS BOND : bond 0.01090 ( 11) SS BOND : angle 1.74350 ( 22) hydrogen bonds : bond 0.04947 ( 571) hydrogen bonds : angle 5.04581 ( 1620) Misc. bond : bond 0.00050 ( 1) link_NAG-ASN : bond 0.00569 ( 14) link_NAG-ASN : angle 4.54270 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.437 Fit side-chains REVERT: v 247 PHE cc_start: 0.7836 (p90) cc_final: 0.7461 (p90) REVERT: v 315 GLN cc_start: 0.7668 (mp10) cc_final: 0.7343 (mp10) REVERT: v 317 MET cc_start: 0.8123 (mpt) cc_final: 0.7430 (mmm) REVERT: v 498 GLU cc_start: 0.8596 (pp20) cc_final: 0.7883 (pp20) REVERT: v 564 GLU cc_start: 0.8467 (pt0) cc_final: 0.8196 (pt0) outliers start: 38 outliers final: 35 residues processed: 107 average time/residue: 0.0894 time to fit residues: 15.4299 Evaluate side-chains 110 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 71 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 chunk 151 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 65 optimal weight: 50.0000 chunk 138 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.216020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.165511 restraints weight = 19464.177| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.80 r_work: 0.3341 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 12669 Z= 0.371 Angle : 0.849 15.198 17398 Z= 0.423 Chirality : 0.055 0.414 2134 Planarity : 0.006 0.089 2315 Dihedral : 8.466 118.132 2250 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.99 % Favored : 91.37 % Rotamer: Outliers : 4.36 % Allowed : 23.13 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1877 helix: 0.02 (0.35), residues: 212 sheet: 0.05 (0.20), residues: 743 loop : -1.45 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.017 0.002 TYR v 375 PHE 0.031 0.003 PHE v 479 TRP 0.021 0.003 TRP C 271 HIS 0.013 0.002 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00899 (12643) covalent geometry : angle 0.82121 (17334) SS BOND : bond 0.00677 ( 11) SS BOND : angle 1.48682 ( 22) hydrogen bonds : bond 0.04228 ( 571) hydrogen bonds : angle 4.82151 ( 1620) Misc. bond : bond 0.00056 ( 1) link_NAG-ASN : bond 0.00563 ( 14) link_NAG-ASN : angle 4.38108 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.13 seconds wall clock time: 64 minutes 28.03 seconds (3868.03 seconds total)