Starting phenix.real_space_refine on Wed Mar 4 16:13:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogl_12883/03_2026/7ogl_12883.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 9269 2.51 5 N 2602 2.21 5 O 2833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14763 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 4899 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 28, 'TRANS': 660} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 12, 'HIS:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4933 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 22, 'ASN:plan1': 2, 'ARG:plan': 14, 'HIS:plan': 3, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 270 Chain: "C" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4928 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 23, 'ASN:plan1': 3, 'ARG:plan': 12, 'HIS:plan': 4, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 269 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.25 Number of scatterers: 14763 At special positions: 0 Unit cell: (109.695, 110.76, 139.515, 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 59 16.00 O 2833 8.00 N 2602 7.00 C 9269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 710.4 milliseconds 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3786 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 37.6% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.697A pdb=" N ILE A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.677A pdb=" N GLN A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.513A pdb=" N LEU A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 312 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.886A pdb=" N GLU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.577A pdb=" N ALA A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 126 through 141 removed outlier: 3.743A pdb=" N ILE B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.678A pdb=" N GLN B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.513A pdb=" N LEU B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 397 through 413 removed outlier: 3.777A pdb=" N HIS B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.587A pdb=" N ALA B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 126 through 141 removed outlier: 3.744A pdb=" N ILE C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.678A pdb=" N GLN C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.512A pdb=" N LEU C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.570A pdb=" N ALA C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 397 through 413 removed outlier: 3.566A pdb=" N ILE C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 564 Processing helix chain 'C' and resid 565 through 570 removed outlier: 4.209A pdb=" N ILE C 569 " --> pdb=" O ILE C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 601 through 616 removed outlier: 3.586A pdb=" N ALA C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 removed outlier: 4.600A pdb=" N ALA C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 651 through 655' Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.615A pdb=" N THR A 20 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR A 60 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA A 115 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN A 62 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 117 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN A 64 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER A 119 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.750A pdb=" N GLY A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 156 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 175 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP A 176 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 191 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 178 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 189 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 180 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU A 190 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N ASP A 508 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N GLU A 192 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N GLN A 506 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLN A 194 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA A 504 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 496 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 505 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 494 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET A 507 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP A 492 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 331 removed outlier: 3.542A pdb=" N GLY A 339 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 432 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 633 removed outlier: 6.930A pdb=" N PHE A 638 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 632 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N GLU A 646 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N LEU A 687 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 648 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG A 686 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 627 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.254A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 60 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA B 115 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN B 62 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 117 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN B 64 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N SER B 119 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.748A pdb=" N GLY B 181 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 156 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 175 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 176 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 191 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 189 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 180 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLN B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA B 504 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 496 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 505 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS B 494 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET B 507 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 492 " --> pdb=" O MET B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.541A pdb=" N GLY B 339 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 432 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 363 through 365 Processing sheet with id=AB2, first strand: chain 'B' and resid 557 through 559 removed outlier: 6.707A pdb=" N THR B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 625 through 632 removed outlier: 11.225A pdb=" N GLY B 627 " --> pdb=" O GLY B 642 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLY B 642 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 629 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 640 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 631 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 641 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU B 687 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 648 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 678 " --> pdb=" O ARG B 686 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER B 688 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 676 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.614A pdb=" N THR C 20 " --> pdb=" O ILE C 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.614A pdb=" N THR C 20 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA C 115 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN C 62 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 117 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.750A pdb=" N GLY C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR C 156 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU C 175 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 176 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 191 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 178 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 189 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 180 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLU C 190 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N ASP C 508 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU C 192 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N GLN C 506 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N GLN C 194 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA C 504 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA C 496 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU C 505 " --> pdb=" O LYS C 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 494 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET C 507 " --> pdb=" O ASP C 492 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C 492 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 327 through 331 removed outlier: 3.542A pdb=" N GLY C 339 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU C 347 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 434 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 432 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 365 Processing sheet with id=AB9, first strand: chain 'C' and resid 554 through 559 removed outlier: 3.654A pdb=" N ALA C 599 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 598 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 586 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 624 through 633 removed outlier: 10.009A pdb=" N THR C 626 " --> pdb=" O GLY C 642 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY C 642 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 628 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 638 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE C 632 " --> pdb=" O GLY C 636 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY C 636 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 641 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE C 685 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 687 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS C 650 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER C 688 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL C 676 " --> pdb=" O SER C 688 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2601 1.28 - 1.42: 3240 1.42 - 1.55: 9000 1.55 - 1.69: 5 1.69 - 1.83: 115 Bond restraints: 14961 Sorted by residual: bond pdb=" C ARG C 325 " pdb=" O ARG C 325 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.07e-02 8.73e+03 5.22e+01 bond pdb=" C THR A 15 " pdb=" O THR A 15 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.14e-02 7.69e+03 5.11e+01 bond pdb=" C ARG B 399 " pdb=" O ARG B 399 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.25e-02 6.40e+03 5.11e+01 bond pdb=" C PRO A 314 " pdb=" O PRO A 314 " ideal model delta sigma weight residual 1.233 1.150 0.083 1.16e-02 7.43e+03 5.08e+01 bond pdb=" C THR C 348 " pdb=" O THR C 348 " ideal model delta sigma weight residual 1.233 1.152 0.082 1.15e-02 7.56e+03 5.04e+01 ... (remaining 14956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 17653 2.82 - 5.64: 2470 5.64 - 8.46: 221 8.46 - 11.28: 35 11.28 - 14.10: 4 Bond angle restraints: 20383 Sorted by residual: angle pdb=" N GLU B 485 " pdb=" CA GLU B 485 " pdb=" C GLU B 485 " ideal model delta sigma weight residual 112.59 98.49 14.10 1.22e+00 6.72e-01 1.34e+02 angle pdb=" N PHE C 551 " pdb=" CA PHE C 551 " pdb=" C PHE C 551 " ideal model delta sigma weight residual 112.59 98.51 14.08 1.22e+00 6.72e-01 1.33e+02 angle pdb=" N ARG C 399 " pdb=" CA ARG C 399 " pdb=" C ARG C 399 " ideal model delta sigma weight residual 111.11 99.42 11.69 1.20e+00 6.94e-01 9.50e+01 angle pdb=" N ILE A 273 " pdb=" CA ILE A 273 " pdb=" C ILE A 273 " ideal model delta sigma weight residual 110.62 101.78 8.84 1.02e+00 9.61e-01 7.52e+01 angle pdb=" N ILE B 273 " pdb=" CA ILE B 273 " pdb=" C ILE B 273 " ideal model delta sigma weight residual 110.62 101.78 8.84 1.02e+00 9.61e-01 7.51e+01 ... (remaining 20378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8311 17.92 - 35.84: 567 35.84 - 53.76: 131 53.76 - 71.68: 19 71.68 - 89.60: 10 Dihedral angle restraints: 9038 sinusoidal: 3143 harmonic: 5895 Sorted by residual: dihedral pdb=" C ILE C 401 " pdb=" N ILE C 401 " pdb=" CA ILE C 401 " pdb=" CB ILE C 401 " ideal model delta harmonic sigma weight residual -122.00 -141.40 19.40 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" C ILE B 401 " pdb=" N ILE B 401 " pdb=" CA ILE B 401 " pdb=" CB ILE B 401 " ideal model delta harmonic sigma weight residual -122.00 -141.39 19.39 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" C ILE A 401 " pdb=" N ILE A 401 " pdb=" CA ILE A 401 " pdb=" CB ILE A 401 " ideal model delta harmonic sigma weight residual -122.00 -141.38 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1886 0.127 - 0.254: 521 0.254 - 0.380: 70 0.380 - 0.507: 4 0.507 - 0.634: 3 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ILE B 401 " pdb=" N ILE B 401 " pdb=" C ILE B 401 " pdb=" CB ILE B 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ILE C 401 " pdb=" N ILE C 401 " pdb=" C ILE C 401 " pdb=" CB ILE C 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 2481 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 128 " 0.026 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C ILE C 128 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE C 128 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL C 129 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 128 " 0.025 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C ILE B 128 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE B 128 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL B 129 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 16 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C VAL B 16 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL B 16 " 0.032 2.00e-02 2.50e+03 pdb=" N THR B 17 " 0.028 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 308 2.65 - 3.21: 13394 3.21 - 3.77: 21001 3.77 - 4.34: 28762 4.34 - 4.90: 46933 Nonbonded interactions: 110398 Sorted by model distance: nonbonded pdb=" O ASP C 492 " pdb=" OD1 ASP C 492 " model vdw 2.082 3.040 nonbonded pdb=" O ASP A 492 " pdb=" OD1 ASP A 492 " model vdw 2.083 3.040 nonbonded pdb=" O ASP B 492 " pdb=" OD1 ASP B 492 " model vdw 2.083 3.040 nonbonded pdb=" O LYS A 321 " pdb=" OD1 ASP A 322 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASP A 486 " pdb=" N HIS A 487 " model vdw 2.206 3.120 ... (remaining 110393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 35 or (resid 36 through 37 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 291 or (resid 292 throug \ h 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thro \ ugh 318 or (resid 319 through 323 and (name N or name CA or name C or name O or \ name CB )) or resid 324 through 402 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 434 or (resid 435 and (name N or \ name CA or name C or name O or name CB )) or resid 436 through 546 or (resid 54 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 548 through \ 549 or (resid 550 and (name N or name CA or name C or name O or name CB )) or re \ sid 551 through 553 or (resid 554 and (name N or name CA or name C or name O or \ name CB )) or resid 555 through 560 or (resid 561 and (name N or name CA or name \ C or name O or name CB )) or resid 562 or (resid 563 through 564 and (name N or \ name CA or name C or name O or name CB )) or resid 565 through 566 or (resid 56 \ 7 through 569 and (name N or name CA or name C or name O or name CB )) or resid \ 570 through 595 or (resid 596 and (name N or name CA or name C or name O or name \ CB )) or resid 597 through 600 or (resid 601 and (name N or name CA or name C o \ r name O or name CB )) or resid 602 or (resid 603 through 608 and (name N or nam \ e CA or name C or name O or name CB )) or resid 609 through 689)) selection = (chain 'B' and (resid 1 through 291 or (resid 292 through 293 and (name N or nam \ e CA or name C or name O or name CB )) or resid 294 through 402 or (resid 403 an \ d (name N or name CA or name C or name O or name CB )) or resid 404 through 434 \ or (resid 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 549 or (resid 550 and (name N or name CA or name C or name O or name \ CB )) or resid 551 through 556 or (resid 557 through 559 and (name N or name CA \ or name C or name O or name CB )) or resid 560 through 567 or (resid 568 throug \ h 569 and (name N or name CA or name C or name O or name CB )) or resid 570 or ( \ resid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 \ through 588 or (resid 589 through 592 and (name N or name CA or name C or name O \ or name CB )) or resid 593 through 618 or (resid 619 through 621 and (name N or \ name CA or name C or name O or name CB )) or (resid 622 through 626 and (name N \ or name CA or name C or name O or name CB )) or (resid 627 through 635 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 636 through 641 and ( \ name N or name CA or name C or name O or name CB )) or (resid 642 through 668 an \ d (name N or name CA or name C or name O or name CB )) or (resid 669 through 672 \ and (name N or name CA or name C or name O or name CB )) or resid 673 or (resid \ 674 through 682 and (name N or name CA or name C or name O or name CB )) or (re \ sid 683 through 689 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 1 through 318 or (resid 319 through 323 and (name N or nam \ e CA or name C or name O or name CB )) or resid 324 through 553 or (resid 554 an \ d (name N or name CA or name C or name O or name CB )) or resid 555 through 556 \ or (resid 557 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 588 or (resid 589 through 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 618 or (resid 619 through 62 \ 1 and (name N or name CA or name C or name O or name CB )) or (resid 622 through \ 626 and (name N or name CA or name C or name O or name CB )) or (resid 627 thro \ ugh 635 and (name N or name CA or name C or name O or name CB )) or (resid 636 t \ hrough 641 and (name N or name CA or name C or name O or name CB )) or (resid 64 \ 2 through 668 and (name N or name CA or name C or name O or name CB )) or (resid \ 669 through 672 and (name N or name CA or name C or name O or name CB )) or res \ id 673 or (resid 674 through 682 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 683 through 689 and (name N or name CA or name C or name O o \ r name CB )))) } 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=0.50 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.190 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.016 0.089 14961 Z= 1.200 Angle : 1.972 14.099 20383 Z= 1.441 Chirality : 0.116 0.634 2484 Planarity : 0.010 0.052 2692 Dihedral : 13.712 89.601 5252 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.70 % Allowed : 6.53 % Favored : 91.77 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2073 helix: -1.34 (0.18), residues: 611 sheet: 0.55 (0.24), residues: 411 loop : -0.91 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 259 TYR 0.034 0.008 TYR C 380 PHE 0.031 0.008 PHE C 343 TRP 0.022 0.007 TRP C 233 HIS 0.013 0.003 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.01569 (14961) covalent geometry : angle 1.97244 (20383) hydrogen bonds : bond 0.21650 ( 764) hydrogen bonds : angle 7.90307 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 357 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 74 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.7924 (Cg_endo) REVERT: A 174 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7723 (ptpt) REVERT: A 243 ASN cc_start: 0.6610 (t0) cc_final: 0.5884 (m110) REVERT: A 302 LYS cc_start: 0.7281 (mtmt) cc_final: 0.6890 (mttp) REVERT: A 418 MET cc_start: 0.6002 (mmm) cc_final: 0.5600 (mmp) REVERT: A 507 MET cc_start: 0.8218 (mtt) cc_final: 0.7953 (mtp) REVERT: B 1 MET cc_start: 0.4691 (ttp) cc_final: 0.4398 (ttm) REVERT: B 15 THR cc_start: 0.8941 (t) cc_final: 0.8546 (m) REVERT: B 86 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7409 (tt0) REVERT: B 128 ILE cc_start: 0.8706 (pp) cc_final: 0.8280 (mm) REVERT: B 315 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.5958 (mtm110) REVERT: B 389 GLU cc_start: 0.7238 (mt-10) cc_final: 0.5845 (mm-30) REVERT: B 537 MET cc_start: 0.8181 (mtp) cc_final: 0.7711 (mtm) REVERT: B 539 GLN cc_start: 0.7335 (tt0) cc_final: 0.7001 (mt0) REVERT: C 389 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6423 (mm-30) REVERT: C 451 MET cc_start: 0.7404 (mtt) cc_final: 0.7190 (mtt) REVERT: C 510 LYS cc_start: 0.7529 (mttm) cc_final: 0.7156 (mtmt) outliers start: 24 outliers final: 3 residues processed: 373 average time/residue: 0.1531 time to fit residues: 78.3951 Evaluate side-chains 181 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 548 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 234 GLN A 298 HIS A 381 ASN A 525 GLN B 64 GLN B 121 ASN B 146 ASN B 212 GLN B 298 HIS B 381 ASN B 520 GLN C 64 GLN C 146 ASN C 160 GLN C 200 GLN C 381 ASN C 542 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151325 restraints weight = 17025.055| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.96 r_work: 0.3462 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14961 Z= 0.152 Angle : 0.620 6.495 20383 Z= 0.342 Chirality : 0.047 0.179 2484 Planarity : 0.004 0.050 2692 Dihedral : 5.618 57.192 2213 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 10.57 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2073 helix: 0.86 (0.20), residues: 628 sheet: 0.79 (0.23), residues: 496 loop : -0.70 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 308 TYR 0.024 0.002 TYR B 385 PHE 0.019 0.002 PHE A 145 TRP 0.002 0.001 TRP C 233 HIS 0.005 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00315 (14961) covalent geometry : angle 0.61991 (20383) hydrogen bonds : bond 0.05516 ( 764) hydrogen bonds : angle 4.92480 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.557 Fit side-chains REVERT: A 3 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7181 (p0) REVERT: A 161 TYR cc_start: 0.8752 (m-80) cc_final: 0.8489 (m-80) REVERT: A 243 ASN cc_start: 0.7164 (t0) cc_final: 0.6529 (m-40) REVERT: B 1 MET cc_start: 0.5022 (ttp) cc_final: 0.4626 (ttm) REVERT: B 128 ILE cc_start: 0.8651 (pp) cc_final: 0.8339 (mm) REVERT: B 259 ARG cc_start: 0.7051 (mtt90) cc_final: 0.6498 (mmm160) REVERT: B 389 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6562 (mm-30) REVERT: B 418 MET cc_start: 0.8350 (tpt) cc_final: 0.8072 (tpp) REVERT: B 537 MET cc_start: 0.8574 (mtp) cc_final: 0.8085 (mtm) REVERT: C 347 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7913 (pm20) REVERT: C 430 GLU cc_start: 0.8064 (mp0) cc_final: 0.7701 (mt-10) REVERT: C 510 LYS cc_start: 0.7679 (mttm) cc_final: 0.7392 (mtmt) outliers start: 32 outliers final: 13 residues processed: 217 average time/residue: 0.1214 time to fit residues: 39.4274 Evaluate side-chains 166 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 170 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 298 HIS B 239 ASN B 298 HIS B 403 HIS B 474 ASN C 209 HIS C 212 GLN C 520 GLN C 524 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147389 restraints weight = 17343.038| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.93 r_work: 0.3400 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14961 Z= 0.148 Angle : 0.556 5.953 20383 Z= 0.301 Chirality : 0.046 0.179 2484 Planarity : 0.004 0.045 2692 Dihedral : 4.909 56.253 2208 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.63 % Allowed : 12.70 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 2073 helix: 1.60 (0.20), residues: 635 sheet: 0.86 (0.24), residues: 500 loop : -0.67 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 409 TYR 0.015 0.002 TYR B 380 PHE 0.017 0.002 PHE A 145 TRP 0.007 0.001 TRP A 233 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00335 (14961) covalent geometry : angle 0.55606 (20383) hydrogen bonds : bond 0.04642 ( 764) hydrogen bonds : angle 4.31933 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.468 Fit side-chains REVERT: A 243 ASN cc_start: 0.7280 (t0) cc_final: 0.6668 (m-40) REVERT: A 418 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6439 (mmm) REVERT: B 1 MET cc_start: 0.5278 (ttp) cc_final: 0.4681 (ttm) REVERT: B 249 LEU cc_start: 0.6562 (mt) cc_final: 0.6259 (tt) REVERT: B 259 ARG cc_start: 0.7132 (mtt90) cc_final: 0.6587 (mmm160) REVERT: B 281 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5327 (tp) REVERT: B 418 MET cc_start: 0.8552 (tpt) cc_final: 0.8068 (tpt) REVERT: B 420 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6400 (tptt) REVERT: B 423 TYR cc_start: 0.9278 (m-80) cc_final: 0.9050 (m-80) REVERT: B 508 ASP cc_start: 0.7807 (t0) cc_final: 0.7589 (m-30) REVERT: B 538 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 40 VAL cc_start: 0.9431 (p) cc_final: 0.9226 (t) REVERT: C 319 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8283 (ptt90) REVERT: C 322 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7853 (p0) REVERT: C 324 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8134 (mp) REVERT: C 430 GLU cc_start: 0.8133 (mp0) cc_final: 0.7856 (mt-10) REVERT: C 510 LYS cc_start: 0.7821 (mttm) cc_final: 0.7438 (mtmt) outliers start: 37 outliers final: 18 residues processed: 199 average time/residue: 0.1149 time to fit residues: 34.6913 Evaluate side-chains 172 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 212 GLN A 298 HIS B 239 ASN B 474 ASN C 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152152 restraints weight = 17488.127| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.60 r_work: 0.3372 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14961 Z= 0.220 Angle : 0.608 9.982 20383 Z= 0.323 Chirality : 0.048 0.224 2484 Planarity : 0.004 0.045 2692 Dihedral : 4.783 24.206 2203 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.55 % Allowed : 14.05 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2073 helix: 1.43 (0.20), residues: 634 sheet: 0.62 (0.23), residues: 511 loop : -0.78 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 530 TYR 0.021 0.002 TYR B 380 PHE 0.018 0.002 PHE B 207 TRP 0.010 0.001 TRP C 233 HIS 0.029 0.002 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00542 (14961) covalent geometry : angle 0.60767 (20383) hydrogen bonds : bond 0.05111 ( 764) hydrogen bonds : angle 4.33351 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.560 Fit side-chains REVERT: A 51 LYS cc_start: 0.6847 (tttm) cc_final: 0.6301 (mttt) REVERT: A 138 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 243 ASN cc_start: 0.7436 (t0) cc_final: 0.6929 (m-40) REVERT: A 344 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8654 (m) REVERT: A 418 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6581 (mmm) REVERT: B 1 MET cc_start: 0.5747 (ttp) cc_final: 0.5112 (ttm) REVERT: B 259 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6936 (mtp180) REVERT: B 418 MET cc_start: 0.8690 (tpt) cc_final: 0.8142 (tpt) REVERT: B 420 LYS cc_start: 0.7224 (ttpt) cc_final: 0.6596 (tptt) REVERT: B 538 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7947 (tm-30) REVERT: C 405 ARG cc_start: 0.8318 (tpt170) cc_final: 0.8057 (tpt170) REVERT: C 597 ILE cc_start: 0.1906 (OUTLIER) cc_final: 0.1238 (mt) outliers start: 50 outliers final: 28 residues processed: 187 average time/residue: 0.1216 time to fit residues: 34.1833 Evaluate side-chains 176 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 179 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154871 restraints weight = 17426.196| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.58 r_work: 0.3423 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.116 Angle : 0.509 8.032 20383 Z= 0.270 Chirality : 0.044 0.186 2484 Planarity : 0.004 0.041 2692 Dihedral : 4.426 23.067 2203 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 15.12 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 2073 helix: 1.76 (0.20), residues: 635 sheet: 0.79 (0.24), residues: 502 loop : -0.71 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 266 TYR 0.013 0.002 TYR B 380 PHE 0.013 0.001 PHE C 78 TRP 0.006 0.001 TRP C 233 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00262 (14961) covalent geometry : angle 0.50942 (20383) hydrogen bonds : bond 0.04159 ( 764) hydrogen bonds : angle 4.07394 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.525 Fit side-chains REVERT: A 32 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8658 (ttp) REVERT: A 51 LYS cc_start: 0.7057 (tttm) cc_final: 0.6330 (mttt) REVERT: A 138 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 243 ASN cc_start: 0.7318 (t0) cc_final: 0.6656 (m-40) REVERT: A 418 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6809 (mmm) REVERT: B 1 MET cc_start: 0.5747 (ttp) cc_final: 0.5003 (ttm) REVERT: B 259 ARG cc_start: 0.7490 (mtt90) cc_final: 0.6982 (mtp180) REVERT: B 369 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.5743 (ptp) REVERT: B 418 MET cc_start: 0.8657 (tpt) cc_final: 0.8024 (tpt) REVERT: B 420 LYS cc_start: 0.7372 (ttpt) cc_final: 0.6566 (tptt) REVERT: B 538 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8250 (tm-30) REVERT: C 324 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8200 (mp) REVERT: C 597 ILE cc_start: 0.1179 (OUTLIER) cc_final: 0.0636 (mt) outliers start: 35 outliers final: 22 residues processed: 175 average time/residue: 0.1197 time to fit residues: 31.7932 Evaluate side-chains 173 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 169 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 298 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134268 restraints weight = 17370.955| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.03 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14961 Z= 0.177 Angle : 0.563 10.061 20383 Z= 0.296 Chirality : 0.046 0.224 2484 Planarity : 0.004 0.044 2692 Dihedral : 4.551 25.666 2203 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.48 % Allowed : 15.40 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2073 helix: 1.54 (0.20), residues: 642 sheet: 0.80 (0.24), residues: 491 loop : -0.83 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 266 TYR 0.021 0.002 TYR C 380 PHE 0.013 0.002 PHE A 145 TRP 0.009 0.001 TRP A 233 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00428 (14961) covalent geometry : angle 0.56297 (20383) hydrogen bonds : bond 0.04687 ( 764) hydrogen bonds : angle 4.12026 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.528 Fit side-chains REVERT: A 51 LYS cc_start: 0.7132 (tttm) cc_final: 0.6412 (mttp) REVERT: A 91 ILE cc_start: 0.9059 (mm) cc_final: 0.8719 (mt) REVERT: A 243 ASN cc_start: 0.7435 (t0) cc_final: 0.7054 (m110) REVERT: A 344 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8792 (m) REVERT: A 418 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6878 (mmm) REVERT: B 259 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7020 (mtt-85) REVERT: B 281 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5460 (tp) REVERT: B 418 MET cc_start: 0.8736 (tpt) cc_final: 0.8158 (tpt) REVERT: B 538 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 666 LEU cc_start: 0.1643 (OUTLIER) cc_final: 0.1413 (pp) REVERT: C 389 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6947 (mm-30) REVERT: C 418 MET cc_start: 0.7437 (mtp) cc_final: 0.6914 (tpt) REVERT: C 597 ILE cc_start: 0.1245 (OUTLIER) cc_final: 0.0702 (mt) outliers start: 49 outliers final: 31 residues processed: 177 average time/residue: 0.1126 time to fit residues: 30.5368 Evaluate side-chains 177 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 chunk 113 optimal weight: 0.9990 chunk 201 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.180852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139388 restraints weight = 17297.970| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.05 r_work: 0.3239 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.129 Angle : 0.510 11.273 20383 Z= 0.267 Chirality : 0.045 0.177 2484 Planarity : 0.004 0.038 2692 Dihedral : 4.281 24.594 2203 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.77 % Allowed : 16.39 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2073 helix: 1.79 (0.20), residues: 646 sheet: 0.87 (0.24), residues: 491 loop : -0.76 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 266 TYR 0.014 0.002 TYR C 380 PHE 0.013 0.001 PHE C 78 TRP 0.007 0.001 TRP A 233 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00304 (14961) covalent geometry : angle 0.50959 (20383) hydrogen bonds : bond 0.04023 ( 764) hydrogen bonds : angle 3.91255 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.566 Fit side-chains REVERT: A 51 LYS cc_start: 0.7250 (tttm) cc_final: 0.6542 (mttp) REVERT: A 243 ASN cc_start: 0.7449 (t0) cc_final: 0.7158 (m110) REVERT: A 277 THR cc_start: 0.7693 (m) cc_final: 0.7387 (m) REVERT: A 344 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8819 (m) REVERT: A 418 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6896 (mmm) REVERT: B 259 ARG cc_start: 0.7529 (mtt90) cc_final: 0.7006 (mtt-85) REVERT: B 538 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 51 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5449 (mtmm) REVERT: C 324 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8147 (mp) REVERT: C 418 MET cc_start: 0.7436 (mtp) cc_final: 0.7025 (tpt) REVERT: C 597 ILE cc_start: 0.1614 (OUTLIER) cc_final: 0.0988 (mt) outliers start: 39 outliers final: 28 residues processed: 177 average time/residue: 0.1099 time to fit residues: 29.8125 Evaluate side-chains 176 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 HIS C 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133815 restraints weight = 17486.485| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.00 r_work: 0.3176 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14961 Z= 0.204 Angle : 0.582 11.990 20383 Z= 0.304 Chirality : 0.047 0.219 2484 Planarity : 0.004 0.043 2692 Dihedral : 4.512 26.200 2203 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.19 % Allowed : 16.04 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2073 helix: 1.66 (0.20), residues: 641 sheet: 0.72 (0.24), residues: 480 loop : -0.90 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 530 TYR 0.022 0.002 TYR C 380 PHE 0.014 0.002 PHE B 207 TRP 0.010 0.001 TRP A 233 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00504 (14961) covalent geometry : angle 0.58222 (20383) hydrogen bonds : bond 0.04765 ( 764) hydrogen bonds : angle 4.05250 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.524 Fit side-chains REVERT: A 51 LYS cc_start: 0.7182 (tttm) cc_final: 0.6470 (mttp) REVERT: A 243 ASN cc_start: 0.7614 (t0) cc_final: 0.7150 (m-40) REVERT: A 277 THR cc_start: 0.7737 (m) cc_final: 0.7522 (m) REVERT: A 344 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 418 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7109 (mmm) REVERT: A 466 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7547 (mmm) REVERT: B 259 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7026 (mtt-85) REVERT: B 538 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 198 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: C 389 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6753 (mm-30) REVERT: C 418 MET cc_start: 0.7413 (mtp) cc_final: 0.7012 (tpt) REVERT: C 597 ILE cc_start: 0.1513 (OUTLIER) cc_final: 0.0974 (mt) outliers start: 45 outliers final: 29 residues processed: 170 average time/residue: 0.1099 time to fit residues: 28.6005 Evaluate side-chains 173 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 199 optimal weight: 30.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 239 ASN B 298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137271 restraints weight = 17379.988| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.120 Angle : 0.507 10.700 20383 Z= 0.265 Chirality : 0.044 0.147 2484 Planarity : 0.003 0.039 2692 Dihedral : 4.193 24.658 2203 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.41 % Allowed : 17.25 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 2073 helix: 1.96 (0.20), residues: 640 sheet: 0.92 (0.25), residues: 467 loop : -0.82 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.014 0.001 TYR C 380 PHE 0.014 0.001 PHE C 78 TRP 0.007 0.001 TRP A 233 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00279 (14961) covalent geometry : angle 0.50667 (20383) hydrogen bonds : bond 0.03907 ( 764) hydrogen bonds : angle 3.85284 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.535 Fit side-chains REVERT: A 51 LYS cc_start: 0.7301 (tttm) cc_final: 0.6578 (mttp) REVERT: A 239 ASN cc_start: 0.4321 (m-40) cc_final: 0.3960 (t0) REVERT: A 243 ASN cc_start: 0.7441 (t0) cc_final: 0.7118 (m110) REVERT: A 277 THR cc_start: 0.7647 (m) cc_final: 0.7423 (m) REVERT: A 344 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8793 (m) REVERT: A 418 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7154 (mmm) REVERT: A 466 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7634 (mmm) REVERT: B 259 ARG cc_start: 0.7526 (mtt90) cc_final: 0.6982 (mtt-85) REVERT: B 538 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 51 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.5527 (mtmm) REVERT: C 324 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8021 (mt) REVERT: C 418 MET cc_start: 0.7377 (mtp) cc_final: 0.7102 (mmm) REVERT: C 597 ILE cc_start: 0.1374 (OUTLIER) cc_final: 0.0870 (mt) outliers start: 34 outliers final: 25 residues processed: 174 average time/residue: 0.1100 time to fit residues: 29.6516 Evaluate side-chains 171 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 14 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 64 optimal weight: 50.0000 chunk 198 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 151 optimal weight: 0.0070 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135057 restraints weight = 17359.262| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.08 r_work: 0.3296 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.109 Angle : 0.499 10.722 20383 Z= 0.260 Chirality : 0.044 0.146 2484 Planarity : 0.003 0.039 2692 Dihedral : 4.050 23.681 2203 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.41 % Allowed : 17.74 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2073 helix: 2.06 (0.20), residues: 641 sheet: 0.95 (0.24), residues: 484 loop : -0.70 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.012 0.001 TYR C 380 PHE 0.013 0.001 PHE C 78 TRP 0.007 0.001 TRP A 233 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00250 (14961) covalent geometry : angle 0.49871 (20383) hydrogen bonds : bond 0.03718 ( 764) hydrogen bonds : angle 3.76450 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.518 Fit side-chains REVERT: A 51 LYS cc_start: 0.7283 (tttm) cc_final: 0.6580 (mttp) REVERT: A 243 ASN cc_start: 0.7347 (t0) cc_final: 0.7113 (m110) REVERT: A 344 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8810 (m) REVERT: A 418 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7185 (mmm) REVERT: A 466 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.7666 (mmm) REVERT: B 259 ARG cc_start: 0.7538 (mtt90) cc_final: 0.6980 (mtt-85) REVERT: B 538 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 51 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5486 (mtmm) REVERT: C 324 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 597 ILE cc_start: 0.1449 (OUTLIER) cc_final: 0.0937 (mt) outliers start: 34 outliers final: 26 residues processed: 164 average time/residue: 0.1068 time to fit residues: 27.3157 Evaluate side-chains 171 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138753 restraints weight = 17286.593| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.96 r_work: 0.3285 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.133 Angle : 0.514 10.559 20383 Z= 0.268 Chirality : 0.045 0.147 2484 Planarity : 0.004 0.042 2692 Dihedral : 4.104 24.512 2203 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 17.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 2073 helix: 2.06 (0.20), residues: 641 sheet: 0.96 (0.25), residues: 477 loop : -0.73 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.016 0.002 TYR B 380 PHE 0.013 0.002 PHE C 78 TRP 0.008 0.001 TRP A 233 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00319 (14961) covalent geometry : angle 0.51450 (20383) hydrogen bonds : bond 0.04006 ( 764) hydrogen bonds : angle 3.79653 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.28 seconds wall clock time: 64 minutes 19.88 seconds (3859.88 seconds total)