Starting phenix.real_space_refine on Thu Jul 31 19:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_33390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_33390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_33390.map" model { file = "/net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_33390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq8_33390/07_2025/7xq8_33390.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 13} 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: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 9} 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, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 13} 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: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 9} 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: 8.16, per 1000 atoms: 0.66 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: 2.94 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.42 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: 5.11 Time building geometry restraints manager: 3.52 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 597 or resid 601 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.940 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- 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 : 13.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (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 TRP 0.019 0.002 TRP C 271 HIS 0.004 0.001 HIS A 36 PHE 0.026 0.002 PHE v 485 TYR 0.010 0.001 TYR C 299 ARG 0.002 0.000 ARG v 251 Details of bonding type rmsd link_NAG-ASN : bond 0.13195 ( 14) link_NAG-ASN : angle 6.56464 ( 42) hydrogen bonds : bond 0.23777 ( 571) hydrogen bonds : angle 9.35094 ( 1620) SS BOND : bond 0.02515 ( 11) SS BOND : angle 2.75084 ( 22) covalent geometry : bond 0.00497 (12643) covalent geometry : angle 0.75695 (17334) Misc. bond : bond 0.00009 ( 1) *********************** 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 : 1.233 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: 0.2430 time to fit residues: 38.3311 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 : 1.415 ------------------------------------------------------------------------------- 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 157 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 146 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 40.0000 chunk 109 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 overall best weight: 11.3390 ------------------------------------------------------------------------------- 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 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 386 ASN v 393 HIS v 487 GLN A 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.209125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.167502 restraints weight = 19193.115| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.25 r_work: 0.3342 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 0.312 12669 Z= 1.397 Angle : 1.798 28.919 17398 Z= 0.914 Chirality : 0.114 2.007 2134 Planarity : 0.012 0.128 2315 Dihedral : 11.283 119.243 2264 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.22 % Favored : 89.66 % Rotamer: Outliers : 8.04 % Allowed : 15.64 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.18), residues: 1877 helix: -2.25 (0.28), residues: 220 sheet: -0.61 (0.19), residues: 740 loop : -2.15 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.008 TRP B 76 HIS 0.029 0.006 HIS A 36 PHE 0.082 0.008 PHE v 479 TYR 0.038 0.007 TYR C 500 ARG 0.016 0.002 ARG B 45 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 14) link_NAG-ASN : angle 6.95127 ( 42) hydrogen bonds : bond 0.09216 ( 571) hydrogen bonds : angle 7.26903 ( 1620) SS BOND : bond 0.02186 ( 11) SS BOND : angle 3.10424 ( 22) covalent geometry : bond 0.03361 (12643) covalent geometry : angle 1.76534 (17334) Misc. bond : bond 0.00006 ( 1) *********************** 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 149 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 77 time to evaluate : 1.414 Fit side-chains REVERT: v 262 PHE cc_start: 0.3226 (OUTLIER) cc_final: 0.2111 (m-80) REVERT: v 564 GLU cc_start: 0.8469 (pt0) cc_final: 0.8269 (pt0) REVERT: B 110 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8636 (mp10) outliers start: 72 outliers final: 52 residues processed: 140 average time/residue: 0.2103 time to fit residues: 47.2382 Evaluate side-chains 125 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 71 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain v residue 262 PHE Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR 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 459 PRO 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 530 THR Chi-restraints excluded: chain v residue 535 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 579 VAL Chi-restraints excluded: chain v residue 584 SER 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 65 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 THR 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 104 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 95 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 50.0000 chunk 147 optimal weight: 50.0000 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 174 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 277 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.217166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.170940 restraints weight = 19770.422| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.76 r_work: 0.3355 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 12669 Z= 0.348 Angle : 0.900 18.874 17398 Z= 0.451 Chirality : 0.060 1.271 2134 Planarity : 0.007 0.099 2315 Dihedral : 9.445 118.573 2256 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.73 % Favored : 91.58 % Rotamer: Outliers : 4.25 % Allowed : 20.22 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1877 helix: -0.49 (0.34), residues: 211 sheet: -0.35 (0.19), residues: 740 loop : -1.89 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 76 HIS 0.012 0.002 HIS A 36 PHE 0.031 0.003 PHE C 479 TYR 0.013 0.002 TYR v 375 ARG 0.006 0.001 ARG v 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 14) link_NAG-ASN : angle 5.68324 ( 42) hydrogen bonds : bond 0.04664 ( 571) hydrogen bonds : angle 5.75394 ( 1620) SS BOND : bond 0.00834 ( 11) SS BOND : angle 1.59109 ( 22) covalent geometry : bond 0.00836 (12643) covalent geometry : angle 0.85569 (17334) Misc. bond : bond 0.00004 ( 1) *********************** 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 121 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 1.397 Fit side-chains REVERT: v 315 GLN cc_start: 0.7824 (mp10) cc_final: 0.7464 (mp10) REVERT: v 317 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8109 (mmt) REVERT: v 560 VAL cc_start: 0.8509 (m) cc_final: 0.8056 (m) REVERT: v 564 GLU cc_start: 0.8463 (pt0) cc_final: 0.8226 (pt0) REVERT: B 96 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8481 (mtm) outliers start: 38 outliers final: 23 residues processed: 110 average time/residue: 0.1972 time to fit residues: 34.8193 Evaluate side-chains 101 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 370 THR Chi-restraints excluded: chain C residue 383 THR 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 C residue 585 LEU Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 573 THR Chi-restraints excluded: chain v residue 585 LEU 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 68 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 13 optimal weight: 50.0000 chunk 142 optimal weight: 110.0000 chunk 9 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 106 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 40.0000 chunk 137 optimal weight: 0.6980 chunk 15 optimal weight: 50.0000 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 50.0000 overall best weight: 10.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.208273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160026 restraints weight = 19522.513| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.76 r_work: 0.3193 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 0.303 12669 Z= 1.306 Angle : 1.699 30.730 17398 Z= 0.863 Chirality : 0.102 1.015 2134 Planarity : 0.012 0.122 2315 Dihedral : 10.894 118.828 2254 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.87 % Favored : 88.17 % Rotamer: Outliers : 11.96 % Allowed : 19.33 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.18), residues: 1877 helix: -2.28 (0.28), residues: 218 sheet: -0.66 (0.19), residues: 740 loop : -2.24 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.008 TRP B 76 HIS 0.028 0.006 HIS A 36 PHE 0.078 0.007 PHE v 479 TYR 0.035 0.006 TYR C 500 ARG 0.015 0.002 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.01051 ( 14) link_NAG-ASN : angle 6.70053 ( 42) hydrogen bonds : bond 0.08519 ( 571) hydrogen bonds : angle 6.70308 ( 1620) SS BOND : bond 0.01878 ( 11) SS BOND : angle 2.82522 ( 22) covalent geometry : bond 0.03144 (12643) covalent geometry : angle 1.66665 (17334) Misc. bond : bond 0.00006 ( 1) *********************** 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 180 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 73 time to evaluate : 1.204 Fit side-chains REVERT: C 489 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: v 262 PHE cc_start: 0.4168 (OUTLIER) cc_final: 0.3660 (m-10) REVERT: v 315 GLN cc_start: 0.7918 (mp10) cc_final: 0.7454 (mp10) REVERT: v 410 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: v 564 GLU cc_start: 0.8667 (pt0) cc_final: 0.8381 (pt0) REVERT: v 593 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7586 (tt) REVERT: A 46 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8910 (mp) REVERT: B 73 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7914 (p0) REVERT: B 82 MET cc_start: 0.7301 (mmt) cc_final: 0.7027 (mmt) REVERT: B 93 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7591 (mmmt) REVERT: B 96 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8529 (mtm) REVERT: B 110 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8542 (mp10) outliers start: 107 outliers final: 81 residues processed: 166 average time/residue: 0.1840 time to fit residues: 47.7634 Evaluate side-chains 162 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 72 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 526 GLU 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 590 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain v residue 262 PHE Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 360 THR Chi-restraints excluded: chain v residue 368 LEU Chi-restraints excluded: chain v residue 379 THR Chi-restraints excluded: chain v residue 381 SER Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 390 VAL Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 405 PHE Chi-restraints excluded: chain v residue 410 GLU Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 422 GLU Chi-restraints excluded: chain v residue 429 THR Chi-restraints excluded: chain v residue 453 ASP Chi-restraints excluded: chain v residue 459 PRO Chi-restraints excluded: chain v residue 467 ARG Chi-restraints excluded: chain v residue 472 ILE 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 535 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 570 LEU Chi-restraints excluded: chain v residue 573 THR Chi-restraints excluded: chain v residue 579 VAL Chi-restraints excluded: chain v residue 585 LEU Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 593 LEU Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL 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 46 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 CYS 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 A residue 163 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 96 MET 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 147 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 320.0000 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 175 optimal weight: 0.5980 chunk 173 optimal weight: 0.5980 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 249 ASN ** 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 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.219598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172188 restraints weight = 19548.483| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.85 r_work: 0.3375 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12669 Z= 0.175 Angle : 0.781 16.280 17398 Z= 0.388 Chirality : 0.052 0.666 2134 Planarity : 0.006 0.095 2315 Dihedral : 8.996 118.335 2253 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.41 % Favored : 91.90 % Rotamer: Outliers : 4.92 % Allowed : 23.69 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.19), residues: 1877 helix: -0.30 (0.34), residues: 219 sheet: -0.24 (0.20), residues: 733 loop : -1.82 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 47 HIS 0.008 0.001 HIS v 400 PHE 0.023 0.002 PHE C 479 TYR 0.012 0.002 TYR v 375 ARG 0.005 0.001 ARG v 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 14) link_NAG-ASN : angle 5.24106 ( 42) hydrogen bonds : bond 0.03774 ( 571) hydrogen bonds : angle 5.22588 ( 1620) SS BOND : bond 0.00264 ( 11) SS BOND : angle 1.10426 ( 22) covalent geometry : bond 0.00401 (12643) covalent geometry : angle 0.73718 (17334) Misc. bond : bond 0.00010 ( 1) *********************** 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 127 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: C 253 SER cc_start: 0.8788 (t) cc_final: 0.8563 (m) REVERT: C 299 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: v 564 GLU cc_start: 0.8236 (pt0) cc_final: 0.8008 (pt0) REVERT: A 113 GLU cc_start: 0.7878 (mp0) cc_final: 0.7611 (mp0) REVERT: B 96 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: B 110 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8482 (mp10) outliers start: 44 outliers final: 23 residues processed: 112 average time/residue: 0.1895 time to fit residues: 34.4828 Evaluate side-chains 101 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 122 optimal weight: 0.8980 chunk 89 optimal weight: 120.0000 chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 50.0000 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 186 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** C 400 HIS ** v 268 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 = 0.4686 r_free = 0.4686 target = 0.219300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.172624 restraints weight = 19758.963| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.91 r_work: 0.3370 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12669 Z= 0.194 Angle : 0.747 13.244 17398 Z= 0.372 Chirality : 0.050 0.552 2134 Planarity : 0.005 0.082 2315 Dihedral : 8.420 117.209 2250 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.83 % Favored : 91.69 % Rotamer: Outliers : 4.69 % Allowed : 24.47 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1877 helix: 0.35 (0.36), residues: 218 sheet: -0.07 (0.19), residues: 739 loop : -1.58 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 271 HIS 0.015 0.002 HIS C 400 PHE 0.020 0.002 PHE C 479 TYR 0.015 0.002 TYR v 375 ARG 0.002 0.000 ARG v 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 14) link_NAG-ASN : angle 4.54486 ( 42) hydrogen bonds : bond 0.03565 ( 571) hydrogen bonds : angle 4.84440 ( 1620) SS BOND : bond 0.00466 ( 11) SS BOND : angle 1.20309 ( 22) covalent geometry : bond 0.00459 (12643) covalent geometry : angle 0.71277 (17334) Misc. bond : bond 0.00022 ( 1) *********************** 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 121 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: C 410 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: v 315 GLN cc_start: 0.7698 (mp10) cc_final: 0.7097 (mp10) REVERT: v 564 GLU cc_start: 0.8368 (pt0) cc_final: 0.8143 (pt0) REVERT: B 87 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8420 (tp-100) REVERT: B 96 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (mtm) REVERT: B 110 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8571 (mp10) outliers start: 42 outliers final: 31 residues processed: 110 average time/residue: 0.1818 time to fit residues: 32.5819 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 : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 472 ILE 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 v residue 596 VAL 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 B residue 68 ASN Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 0 optimal weight: 320.0000 chunk 159 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 85 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 chunk 50 optimal weight: 0.1980 chunk 7 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.214793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.162609 restraints weight = 19381.815| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.95 r_work: 0.3292 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.141 12669 Z= 0.490 Angle : 0.957 18.813 17398 Z= 0.481 Chirality : 0.059 0.522 2134 Planarity : 0.007 0.086 2315 Dihedral : 8.983 118.681 2250 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.74 % Favored : 90.62 % Rotamer: Outliers : 6.03 % Allowed : 24.58 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1877 helix: -0.28 (0.34), residues: 218 sheet: -0.15 (0.20), residues: 741 loop : -1.75 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 76 HIS 0.019 0.003 HIS C 400 PHE 0.035 0.003 PHE v 479 TYR 0.019 0.003 TYR v 500 ARG 0.007 0.001 ARG v 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 14) link_NAG-ASN : angle 4.84279 ( 42) hydrogen bonds : bond 0.04803 ( 571) hydrogen bonds : angle 5.13851 ( 1620) SS BOND : bond 0.00942 ( 11) SS BOND : angle 1.79246 ( 22) covalent geometry : bond 0.01187 (12643) covalent geometry : angle 0.92653 (17334) Misc. bond : bond 0.00007 ( 1) *********************** 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 130 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 1.399 Fit side-chains REVERT: C 410 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: v 564 GLU cc_start: 0.8437 (pt0) cc_final: 0.8173 (pt0) REVERT: B 55 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7758 (mtt-85) REVERT: B 96 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8445 (mtm) REVERT: B 110 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8553 (mp10) outliers start: 54 outliers final: 42 residues processed: 118 average time/residue: 0.2113 time to fit residues: 39.2345 Evaluate side-chains 121 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER 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 247 PHE Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 472 ILE 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 570 LEU Chi-restraints excluded: chain v residue 575 SER Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL 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 B residue 55 ARG Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 MET 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 167 optimal weight: 0.5980 chunk 10 optimal weight: 50.0000 chunk 158 optimal weight: 50.0000 chunk 162 optimal weight: 0.6980 chunk 12 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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** ** 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 = 0.4660 r_free = 0.4660 target = 0.216531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.168394 restraints weight = 19616.603| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.92 r_work: 0.3354 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 12669 Z= 0.345 Angle : 0.843 14.628 17398 Z= 0.422 Chirality : 0.054 0.476 2134 Planarity : 0.006 0.077 2315 Dihedral : 8.653 118.043 2250 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.42 % Favored : 90.94 % Rotamer: Outliers : 5.70 % Allowed : 25.59 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1877 helix: -0.13 (0.34), residues: 219 sheet: -0.08 (0.20), residues: 731 loop : -1.64 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 76 HIS 0.009 0.002 HIS A 36 PHE 0.026 0.002 PHE v 479 TYR 0.015 0.002 TYR v 375 ARG 0.005 0.001 ARG v 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 14) link_NAG-ASN : angle 4.63579 ( 42) hydrogen bonds : bond 0.04195 ( 571) hydrogen bonds : angle 4.92750 ( 1620) SS BOND : bond 0.00689 ( 11) SS BOND : angle 1.47460 ( 22) covalent geometry : bond 0.00836 (12643) covalent geometry : angle 0.81144 (17334) Misc. bond : bond 0.00020 ( 1) *********************** 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 131 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 80 time to evaluate : 1.327 Fit side-chains REVERT: C 410 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: v 315 GLN cc_start: 0.7710 (mp10) cc_final: 0.7231 (mp10) REVERT: v 498 GLU cc_start: 0.8578 (pp20) cc_final: 0.7858 (pp20) REVERT: v 564 GLU cc_start: 0.8402 (pt0) cc_final: 0.8148 (pt0) outliers start: 51 outliers final: 41 residues processed: 120 average time/residue: 0.2118 time to fit residues: 39.3386 Evaluate side-chains 119 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 472 ILE 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 570 LEU Chi-restraints excluded: chain v residue 575 SER Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL 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 B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 67 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 108 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 126 optimal weight: 0.7980 chunk 75 optimal weight: 50.0000 chunk 22 optimal weight: 0.1980 chunk 125 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.218460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168771 restraints weight = 19594.934| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.88 r_work: 0.3383 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12669 Z= 0.223 Angle : 0.753 11.976 17398 Z= 0.375 Chirality : 0.051 0.451 2134 Planarity : 0.006 0.089 2315 Dihedral : 8.237 117.380 2249 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.10 % Favored : 91.32 % Rotamer: Outliers : 5.59 % Allowed : 25.92 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1877 helix: 0.32 (0.35), residues: 218 sheet: 0.06 (0.20), residues: 722 loop : -1.50 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 271 HIS 0.006 0.001 HIS A 36 PHE 0.022 0.002 PHE C 479 TYR 0.015 0.002 TYR v 375 ARG 0.006 0.001 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 14) link_NAG-ASN : angle 4.36760 ( 42) hydrogen bonds : bond 0.03631 ( 571) hydrogen bonds : angle 4.68132 ( 1620) SS BOND : bond 0.00479 ( 11) SS BOND : angle 1.34765 ( 22) covalent geometry : bond 0.00539 (12643) covalent geometry : angle 0.72167 (17334) Misc. bond : bond 0.00025 ( 1) *********************** 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 133 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 1.204 Fit side-chains REVERT: C 410 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: v 315 GLN cc_start: 0.7881 (mp10) cc_final: 0.7381 (mp10) REVERT: v 336 MET cc_start: 0.3393 (mmp) cc_final: 0.2132 (tpp) REVERT: v 498 GLU cc_start: 0.8447 (pp20) cc_final: 0.7731 (pp20) REVERT: v 564 GLU cc_start: 0.8161 (pt0) cc_final: 0.7925 (pt0) REVERT: A 113 GLU cc_start: 0.7801 (mp0) cc_final: 0.7552 (mp0) REVERT: B 55 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8231 (mtt90) outliers start: 50 outliers final: 43 residues processed: 120 average time/residue: 0.1980 time to fit residues: 36.7999 Evaluate side-chains 125 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET 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 368 LEU Chi-restraints excluded: chain C residue 370 THR 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 410 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain v residue 247 PHE Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 472 ILE 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 594 PHE Chi-restraints excluded: chain v residue 596 VAL 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 B residue 55 ARG Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 152 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 chunk 159 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 258 GLN ** v 268 GLN ** 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 = 0.4662 r_free = 0.4662 target = 0.216736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168379 restraints weight = 19359.933| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.90 r_work: 0.3351 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 12669 Z= 0.341 Angle : 0.835 14.970 17398 Z= 0.418 Chirality : 0.054 0.443 2134 Planarity : 0.006 0.085 2315 Dihedral : 8.380 118.063 2249 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.20 % Favored : 91.21 % Rotamer: Outliers : 6.26 % Allowed : 25.36 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1877 helix: -0.20 (0.34), residues: 232 sheet: 0.05 (0.20), residues: 721 loop : -1.55 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 271 HIS 0.008 0.002 HIS A 36 PHE 0.026 0.002 PHE v 479 TYR 0.015 0.002 TYR v 375 ARG 0.012 0.001 ARG v 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 14) link_NAG-ASN : angle 4.40127 ( 42) hydrogen bonds : bond 0.04097 ( 571) hydrogen bonds : angle 4.78821 ( 1620) SS BOND : bond 0.00688 ( 11) SS BOND : angle 1.54063 ( 22) covalent geometry : bond 0.00827 (12643) covalent geometry : angle 0.80638 (17334) Misc. bond : bond 0.00030 ( 1) ********************** 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 134 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 78 time to evaluate : 1.423 Fit side-chains REVERT: C 410 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: v 243 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8146 (mmp80) REVERT: v 315 GLN cc_start: 0.7773 (mp10) cc_final: 0.7370 (mp10) REVERT: v 317 MET cc_start: 0.7337 (mmt) cc_final: 0.7060 (mmp) REVERT: v 498 GLU cc_start: 0.8556 (pp20) cc_final: 0.7821 (pp20) REVERT: v 564 GLU cc_start: 0.8388 (pt0) cc_final: 0.8114 (pt0) outliers start: 56 outliers final: 51 residues processed: 121 average time/residue: 0.2069 time to fit residues: 38.8725 Evaluate side-chains 130 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 78 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET 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 368 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 302 THR Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 467 ARG Chi-restraints excluded: chain v residue 472 ILE 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 594 PHE Chi-restraints excluded: chain v residue 596 VAL 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 B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 6 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 158 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 63 optimal weight: 50.0000 chunk 47 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 258 GLN ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.220257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.175546 restraints weight = 19611.642| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.79 r_work: 0.3400 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12669 Z= 0.159 Angle : 0.701 11.969 17398 Z= 0.347 Chirality : 0.049 0.422 2134 Planarity : 0.005 0.080 2315 Dihedral : 7.834 116.727 2249 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.57 % Favored : 91.96 % Rotamer: Outliers : 5.25 % Allowed : 26.59 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1877 helix: 0.35 (0.35), residues: 232 sheet: 0.22 (0.20), residues: 708 loop : -1.39 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 271 HIS 0.005 0.001 HIS A 36 PHE 0.019 0.002 PHE C 479 TYR 0.015 0.001 TYR v 375 ARG 0.009 0.001 ARG v 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 14) link_NAG-ASN : angle 4.13634 ( 42) hydrogen bonds : bond 0.03237 ( 571) hydrogen bonds : angle 4.43694 ( 1620) SS BOND : bond 0.00259 ( 11) SS BOND : angle 1.13175 ( 22) covalent geometry : bond 0.00379 (12643) covalent geometry : angle 0.67073 (17334) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7337.14 seconds wall clock time: 125 minutes 49.11 seconds (7549.11 seconds total)