Starting phenix.real_space_refine on Sat Sep 12 21:52:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oo4_20145/09_2026/6oo4_20145.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 98 5.16 5 C 12156 2.51 5 N 3116 2.21 5 O 3082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18452 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4561 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 15, 'ASN:plan1': 8, 'ARG:plan': 10, 'GLU:plan': 19, 'GLN:plan1': 8, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4573 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 16, 'ASN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 18, 'GLN:plan1': 8, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4561 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 15, 'ASN:plan1': 8, 'ARG:plan': 10, 'GLU:plan': 19, 'GLN:plan1': 8, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 237 Chain: "D" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4573 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 16, 'ASN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 18, 'GLN:plan1': 8, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 226 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18452 At special positions: 0 Unit cell: (155.52, 156.6, 116.64, 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 98 16.00 O 3082 8.00 N 3116 7.00 C 12156 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 617.4 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 4 sheets defined 62.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.576A pdb=" N GLU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.668A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.666A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.899A pdb=" N VAL A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 259 through 280 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.507A pdb=" N GLY A 287 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.557A pdb=" N GLY A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.542A pdb=" N PHE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 373 through 411 removed outlier: 4.506A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 428 through 457 Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.202A pdb=" N LEU A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.673A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 514 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 515 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 516 " --> pdb=" O TYR A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 516' Processing helix chain 'A' and resid 517 through 557 removed outlier: 4.145A pdb=" N TYR A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.939A pdb=" N GLU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.786A pdb=" N VAL A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 672 removed outlier: 4.410A pdb=" N TRP A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.531A pdb=" N LEU B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.684A pdb=" N ASP B 89 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.781A pdb=" N GLY B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.881A pdb=" N GLN B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.634A pdb=" N VAL B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.860A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 removed outlier: 3.763A pdb=" N SER B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.710A pdb=" N ILE B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.518A pdb=" N PHE B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 375 through 411 removed outlier: 3.733A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 428 through 457 Processing helix chain 'B' and resid 468 through 491 Processing helix chain 'B' and resid 494 through 509 removed outlier: 4.023A pdb=" N LEU B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.591A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 516' Processing helix chain 'B' and resid 517 through 534 removed outlier: 4.377A pdb=" N TYR B 523 " --> pdb=" O HIS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.784A pdb=" N GLU B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 648 removed outlier: 3.668A pdb=" N ASN B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 671 removed outlier: 4.271A pdb=" N TRP B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.530A pdb=" N GLY C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.681A pdb=" N ILE C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.685A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.939A pdb=" N VAL C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 259 through 280 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.514A pdb=" N GLY C 287 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.541A pdb=" N GLY C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.542A pdb=" N PHE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 373 through 411 removed outlier: 4.501A pdb=" N LYS C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Proline residue: C 389 - end of helix Processing helix chain 'C' and resid 428 through 457 Processing helix chain 'C' and resid 468 through 490 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.197A pdb=" N LEU C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 3.676A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 514 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 515 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 516 " --> pdb=" O TYR C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 516' Processing helix chain 'C' and resid 517 through 557 removed outlier: 4.146A pdb=" N TYR C 523 " --> pdb=" O HIS C 519 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.933A pdb=" N GLU C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 603 " --> pdb=" O PHE C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 648 removed outlier: 3.787A pdb=" N VAL C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 672 removed outlier: 4.410A pdb=" N TRP C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.747A pdb=" N LEU D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.711A pdb=" N ASP D 89 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 117 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.702A pdb=" N GLY D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.876A pdb=" N GLN D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.600A pdb=" N VAL D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.902A pdb=" N ALA D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 280 removed outlier: 3.754A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.728A pdb=" N ILE D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.566A pdb=" N PHE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 373 through 411 removed outlier: 4.650A pdb=" N LYS D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) Proline residue: D 389 - end of helix Processing helix chain 'D' and resid 428 through 457 Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 494 through 509 removed outlier: 4.033A pdb=" N LEU D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.589A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 514 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY D 516 " --> pdb=" O TYR D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 510 through 516' Processing helix chain 'D' and resid 517 through 534 removed outlier: 4.379A pdb=" N TYR D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 557 Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.796A pdb=" N GLU D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 603 " --> pdb=" O PHE D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 648 removed outlier: 3.773A pdb=" N VAL D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 671 removed outlier: 4.244A pdb=" N TRP D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 333 removed outlier: 6.845A pdb=" N VAL A 338 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS A 332 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 336 " --> pdb=" O CYS A 332 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 690 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG A 700 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 688 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS A 702 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET A 686 " --> pdb=" O CYS A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 327 through 333 removed outlier: 6.822A pdb=" N VAL B 338 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS B 332 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 336 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP B 698 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 327 through 333 removed outlier: 6.846A pdb=" N VAL C 338 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS C 332 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 336 " --> pdb=" O CYS C 332 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 690 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 700 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR C 688 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 702 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N MET C 686 " --> pdb=" O CYS C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 327 through 333 removed outlier: 6.819A pdb=" N VAL D 338 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS D 332 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL D 336 " --> pdb=" O CYS D 332 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP D 698 " --> pdb=" O VAL D 689 " (cutoff:3.500A) 1070 hydrogen bonds defined for protein. 3180 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: 2.90 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2780 1.29 - 1.42: 5194 1.42 - 1.55: 10754 1.55 - 1.69: 42 1.69 - 1.82: 154 Bond restraints: 18924 Sorted by residual: bond pdb=" CAJ 6EU A1001 " pdb=" OAA 6EU A1001 " ideal model delta sigma weight residual 1.439 1.767 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" CAJ 6EU C1001 " pdb=" OAA 6EU C1001 " ideal model delta sigma weight residual 1.439 1.767 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" CAJ 6EU B1001 " pdb=" OAA 6EU B1001 " ideal model delta sigma weight residual 1.439 1.760 -0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" CAJ 6EU D1001 " pdb=" OAA 6EU D1001 " ideal model delta sigma weight residual 1.439 1.760 -0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" CAS 6EU D1001 " pdb=" CAX 6EU D1001 " ideal model delta sigma weight residual 1.334 1.588 -0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 25150 2.81 - 5.61: 588 5.61 - 8.42: 118 8.42 - 11.22: 20 11.22 - 14.03: 6 Bond angle restraints: 25882 Sorted by residual: angle pdb=" N PRO C 413 " pdb=" CA PRO C 413 " pdb=" CB PRO C 413 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.51e+01 angle pdb=" N PRO B 413 " pdb=" CA PRO B 413 " pdb=" CB PRO B 413 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N PRO D 413 " pdb=" CA PRO D 413 " pdb=" CB PRO D 413 " ideal model delta sigma weight residual 103.00 110.33 -7.33 1.10e+00 8.26e-01 4.44e+01 angle pdb=" N PRO A 413 " pdb=" CA PRO A 413 " pdb=" CB PRO A 413 " ideal model delta sigma weight residual 103.00 110.32 -7.32 1.10e+00 8.26e-01 4.43e+01 angle pdb=" CA GLN A 412 " pdb=" C GLN A 412 " pdb=" N PRO A 413 " ideal model delta sigma weight residual 120.58 116.82 3.76 7.40e-01 1.83e+00 2.58e+01 ... (remaining 25877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 10412 14.94 - 29.89: 431 29.89 - 44.83: 58 44.83 - 59.78: 10 59.78 - 74.72: 11 Dihedral angle restraints: 10922 sinusoidal: 3790 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N GLY C 208 " pdb=" CA GLY C 208 " ideal model delta harmonic sigma weight residual 180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N GLY A 208 " pdb=" CA GLY A 208 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER C 258 " pdb=" C SER C 258 " pdb=" N ALA C 259 " pdb=" CA ALA C 259 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 10919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2456 0.066 - 0.131: 498 0.131 - 0.197: 60 0.197 - 0.263: 8 0.263 - 0.329: 16 Chirality restraints: 3038 Sorted by residual: chirality pdb=" CAN 6EU A1001 " pdb=" CAJ 6EU A1001 " pdb=" CAP 6EU A1001 " pdb=" CAT 6EU A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.81 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CAL 6EU A1001 " pdb=" CAK 6EU A1001 " pdb=" CAM 6EU A1001 " pdb=" OAB 6EU A1001 " both_signs ideal model delta sigma weight residual False 2.77 2.44 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CAL 6EU C1001 " pdb=" CAK 6EU C1001 " pdb=" CAM 6EU C1001 " pdb=" OAB 6EU C1001 " both_signs ideal model delta sigma weight residual False 2.77 2.45 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 3035 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 405 " -0.022 2.00e-02 2.50e+03 2.02e-02 7.16e+00 pdb=" CG PHE A 405 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 405 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 405 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 405 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 405 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 405 " -0.022 2.00e-02 2.50e+03 1.99e-02 6.90e+00 pdb=" CG PHE B 405 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 405 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 405 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 405 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 405 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 405 " -0.021 2.00e-02 2.50e+03 1.97e-02 6.79e+00 pdb=" CG PHE C 405 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 405 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 405 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 405 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 405 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 405 " -0.003 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 12 2.47 - 3.07: 10992 3.07 - 3.68: 26556 3.68 - 4.29: 36796 4.29 - 4.90: 64338 Nonbonded interactions: 138694 Sorted by model distance: nonbonded pdb=" O ALA D 255 " pdb=" CE LYS D 305 " model vdw 1.858 3.440 nonbonded pdb=" O ALA C 255 " pdb=" CE LYS C 305 " model vdw 2.038 3.440 nonbonded pdb=" O ALA A 255 " pdb=" CE LYS A 305 " model vdw 2.047 3.440 nonbonded pdb=" O ALA B 255 " pdb=" CE LYS B 305 " model vdw 2.185 3.440 nonbonded pdb=" OG SER B 258 " pdb=" N ASN B 261 " model vdw 2.362 3.120 ... (remaining 138689 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 93 or (resid 94 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 107 or (resid 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 156 or \ (resid 157 through 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 1001)) selection = (chain 'B' and (resid 73 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 237 or \ (resid 238 through 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 257 or (resid 258 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 302 or (resid \ 303 and (name N or name CA or name C or name O or name CB )) or resid 304 throug \ h 362 or (resid 363 through 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 1001)) selection = (chain 'C' and (resid 73 through 93 or (resid 94 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 107 or (resid 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 156 or \ (resid 157 through 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 1001)) selection = (chain 'D' and (resid 73 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 237 or \ (resid 238 through 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 257 or (resid 258 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 302 or (resid \ 303 and (name N or name CA or name C or name O or name CB )) or resid 304 throug \ h 362 or (resid 363 through 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.020 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 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 : 0.013 0.328 18926 Z= 0.594 Angle : 1.103 14.028 25882 Z= 0.575 Chirality : 0.058 0.329 3038 Planarity : 0.007 0.061 3180 Dihedral : 9.305 74.723 6314 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.13), residues: 2408 helix: -1.43 (0.11), residues: 1392 sheet: 0.89 (0.54), residues: 68 loop : -2.75 (0.14), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 456 TYR 0.031 0.004 TYR D 160 PHE 0.046 0.004 PHE A 405 TRP 0.024 0.003 TRP B 713 HIS 0.011 0.003 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01290 / 0.59 (18924) covalent geometry : angle 1.10306 / 0.57 (25882) hydrogen bonds : bond 0.15260 / 10.46 ( 1070) hydrogen bonds : angle 5.31659 / 3.77 ( 3180) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.741 Fit side-chains REVERT: A 120 MET cc_start: 0.5498 (mtt) cc_final: 0.5264 (mtt) REVERT: A 133 CYS cc_start: 0.7196 (t) cc_final: 0.6850 (p) REVERT: A 195 HIS cc_start: 0.6220 (t-90) cc_final: 0.5621 (t70) REVERT: A 209 GLU cc_start: 0.6460 (mp0) cc_final: 0.6234 (mm-30) REVERT: A 221 TRP cc_start: 0.6424 (t-100) cc_final: 0.5955 (t-100) REVERT: A 225 ASN cc_start: 0.6552 (t0) cc_final: 0.6332 (m110) REVERT: A 270 ASP cc_start: 0.7713 (m-30) cc_final: 0.7459 (m-30) REVERT: A 337 ARG cc_start: 0.6385 (ptp-170) cc_final: 0.6182 (ptm160) REVERT: A 347 ASP cc_start: 0.7763 (t0) cc_final: 0.7314 (t0) REVERT: A 349 TRP cc_start: 0.7941 (t60) cc_final: 0.7741 (t60) REVERT: A 386 ARG cc_start: 0.7454 (ttt180) cc_final: 0.7143 (ttp80) REVERT: A 526 MET cc_start: 0.6395 (mmm) cc_final: 0.5917 (mtt) REVERT: A 613 GLN cc_start: 0.7683 (mt0) cc_final: 0.7413 (pm20) REVERT: A 692 ARG cc_start: 0.6945 (mtp180) cc_final: 0.5984 (mtm-85) REVERT: A 699 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 238 GLN cc_start: 0.8054 (mt0) cc_final: 0.7801 (mt0) REVERT: B 286 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7120 (mt-10) REVERT: B 381 GLN cc_start: 0.5893 (tp-100) cc_final: 0.5410 (tp-100) REVERT: B 452 TRP cc_start: 0.6584 (t60) cc_final: 0.6333 (t60) REVERT: B 455 TRP cc_start: 0.7606 (t-100) cc_final: 0.7056 (t-100) REVERT: B 526 MET cc_start: 0.6435 (mmm) cc_final: 0.6074 (mtt) REVERT: B 617 ARG cc_start: 0.7066 (ptt-90) cc_final: 0.6828 (ptt-90) REVERT: B 724 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6593 (mm-30) REVERT: C 120 MET cc_start: 0.5422 (mtt) cc_final: 0.5103 (mtt) REVERT: C 121 LYS cc_start: 0.7545 (tttp) cc_final: 0.7342 (tptp) REVERT: C 161 ARG cc_start: 0.5500 (ttt90) cc_final: 0.5249 (ttp80) REVERT: C 195 HIS cc_start: 0.6445 (t-90) cc_final: 0.5700 (t70) REVERT: C 232 HIS cc_start: 0.6501 (m90) cc_final: 0.6226 (m90) REVERT: C 270 ASP cc_start: 0.7522 (m-30) cc_final: 0.7194 (m-30) REVERT: C 347 ASP cc_start: 0.7476 (t0) cc_final: 0.7069 (t0) REVERT: C 386 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6672 (mtt90) REVERT: C 526 MET cc_start: 0.6570 (mmm) cc_final: 0.6280 (mtt) REVERT: C 613 GLN cc_start: 0.7631 (mt0) cc_final: 0.7368 (pm20) REVERT: C 637 ASN cc_start: 0.7077 (t0) cc_final: 0.6875 (t0) REVERT: C 674 TRP cc_start: 0.8467 (p-90) cc_final: 0.8248 (p-90) REVERT: C 686 MET cc_start: 0.7738 (tmm) cc_final: 0.7526 (tmm) REVERT: C 692 ARG cc_start: 0.6833 (mtp180) cc_final: 0.5883 (mtt90) REVERT: C 699 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7106 (mt-10) REVERT: D 104 LEU cc_start: 0.6677 (mt) cc_final: 0.6350 (mp) REVERT: D 187 ASN cc_start: 0.6908 (t0) cc_final: 0.6613 (t0) REVERT: D 236 SER cc_start: 0.7807 (t) cc_final: 0.7365 (p) REVERT: D 452 TRP cc_start: 0.6693 (t60) cc_final: 0.6244 (t60) REVERT: D 455 TRP cc_start: 0.7302 (t-100) cc_final: 0.6766 (t-100) REVERT: D 526 MET cc_start: 0.6515 (mmm) cc_final: 0.6175 (mtt) REVERT: D 709 ASN cc_start: 0.7851 (t0) cc_final: 0.7603 (t0) REVERT: D 724 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6576 (mm-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1487 time to fit residues: 62.3566 Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 261 ASN C 519 HIS D 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119959 restraints weight = 23425.719| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.68 r_work: 0.3041 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18926 Z= 0.153 Angle : 0.593 8.405 25882 Z= 0.299 Chirality : 0.038 0.141 3038 Planarity : 0.004 0.046 3180 Dihedral : 5.697 57.763 2656 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.65 % Allowed : 4.88 % Favored : 94.48 % 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: -0.24 (0.16), residues: 2408 helix: 0.98 (0.13), residues: 1420 sheet: 1.06 (0.55), residues: 68 loop : -2.15 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.014 0.002 TYR D 206 PHE 0.018 0.002 PHE A 309 TRP 0.011 0.001 TRP B 507 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18924) covalent geometry : angle 0.59285 / 0.30 (25882) hydrogen bonds : bond 0.05734 / 3.80 ( 1070) hydrogen bonds : angle 3.57761 / 2.55 ( 3180) Misc. bond : bond 0.00198 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.8336 (t-90) cc_final: 0.7821 (t70) REVERT: A 349 TRP cc_start: 0.9001 (t60) cc_final: 0.8795 (t60) REVERT: A 692 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6927 (mtt90) REVERT: B 121 LYS cc_start: 0.7992 (tptm) cc_final: 0.7565 (tptt) REVERT: B 402 MET cc_start: 0.9108 (mmt) cc_final: 0.8539 (mmp) REVERT: B 640 ILE cc_start: 0.8372 (pt) cc_final: 0.7997 (mm) REVERT: C 135 GLN cc_start: 0.7280 (tt0) cc_final: 0.7067 (tp40) REVERT: C 195 HIS cc_start: 0.8245 (t-90) cc_final: 0.7666 (t70) REVERT: C 386 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8321 (mtt90) REVERT: C 526 MET cc_start: 0.8757 (mmm) cc_final: 0.8525 (mtt) REVERT: C 692 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6791 (mtt90) REVERT: D 236 SER cc_start: 0.8806 (t) cc_final: 0.8383 (p) REVERT: D 452 TRP cc_start: 0.8465 (t60) cc_final: 0.8169 (t60) outliers start: 11 outliers final: 10 residues processed: 211 average time/residue: 0.1197 time to fit residues: 39.9552 Evaluate side-chains 187 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 555 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 231 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 0.0670 chunk 209 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122816 restraints weight = 23431.373| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.68 r_work: 0.3079 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18926 Z= 0.106 Angle : 0.522 8.500 25882 Z= 0.260 Chirality : 0.036 0.138 3038 Planarity : 0.003 0.042 3180 Dihedral : 5.338 69.563 2656 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.06 % Allowed : 6.76 % Favored : 92.19 % 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: 0.79 (0.17), residues: 2408 helix: 1.85 (0.13), residues: 1436 sheet: 1.04 (0.55), residues: 68 loop : -1.81 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 615 TYR 0.012 0.001 TYR D 523 PHE 0.016 0.001 PHE A 309 TRP 0.014 0.001 TRP C 674 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (18924) covalent geometry : angle 0.52192 / 0.26 (25882) hydrogen bonds : bond 0.04417 / 2.94 ( 1070) hydrogen bonds : angle 3.34445 / 2.41 ( 3180) Misc. bond : bond 0.00179 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8384 (tptt) cc_final: 0.8181 (tptt) REVERT: A 125 ASN cc_start: 0.7003 (m110) cc_final: 0.6475 (m110) REVERT: A 514 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 692 ARG cc_start: 0.7503 (mtp180) cc_final: 0.6823 (mtm-85) REVERT: A 699 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8246 (tt0) REVERT: B 121 LYS cc_start: 0.8011 (tptm) cc_final: 0.7582 (tptt) REVERT: B 678 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.5742 (ttp80) REVERT: B 724 GLU cc_start: 0.7891 (pm20) cc_final: 0.7255 (mm-30) REVERT: C 195 HIS cc_start: 0.8171 (t-90) cc_final: 0.7579 (t70) REVERT: C 386 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8278 (mtt90) REVERT: C 452 TRP cc_start: 0.7962 (t60) cc_final: 0.7655 (t60) REVERT: C 692 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6720 (mtt90) REVERT: D 86 ASN cc_start: 0.5861 (m-40) cc_final: 0.5451 (p0) REVERT: D 236 SER cc_start: 0.8803 (t) cc_final: 0.8368 (p) REVERT: D 452 TRP cc_start: 0.8413 (t60) cc_final: 0.8112 (t60) outliers start: 18 outliers final: 8 residues processed: 213 average time/residue: 0.1152 time to fit residues: 39.3112 Evaluate side-chains 191 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 222 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 8 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 127 optimal weight: 0.0030 chunk 170 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 235 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN C 637 ASN D 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116740 restraints weight = 23563.895| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.66 r_work: 0.2997 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18926 Z= 0.187 Angle : 0.588 8.785 25882 Z= 0.293 Chirality : 0.039 0.160 3038 Planarity : 0.004 0.042 3180 Dihedral : 5.366 62.508 2656 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.53 % Allowed : 8.28 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2408 helix: 2.09 (0.14), residues: 1428 sheet: 1.25 (0.57), residues: 68 loop : -1.72 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.014 0.002 TYR B 401 PHE 0.024 0.002 PHE B 405 TRP 0.022 0.001 TRP A 452 HIS 0.007 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (18924) covalent geometry : angle 0.58839 / 0.29 (25882) hydrogen bonds : bond 0.05877 / 3.87 ( 1070) hydrogen bonds : angle 3.39017 / 2.43 ( 3180) Misc. bond : bond 0.00264 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.8715 (p) REVERT: A 692 ARG cc_start: 0.7559 (mtp180) cc_final: 0.6856 (mtm-85) REVERT: A 699 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8287 (tt0) REVERT: B 121 LYS cc_start: 0.8006 (tptm) cc_final: 0.7522 (tptt) REVERT: B 678 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6157 (ttp80) REVERT: B 724 GLU cc_start: 0.7903 (pm20) cc_final: 0.7223 (mm-30) REVERT: C 195 HIS cc_start: 0.8272 (t-90) cc_final: 0.7677 (t70) REVERT: C 386 ARG cc_start: 0.8767 (ttt180) cc_final: 0.8326 (mtt90) REVERT: C 402 MET cc_start: 0.8956 (mmt) cc_final: 0.8597 (mmp) REVERT: C 692 ARG cc_start: 0.7519 (mtp180) cc_final: 0.6828 (mtm-85) REVERT: D 452 TRP cc_start: 0.8510 (t60) cc_final: 0.8171 (t60) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.1260 time to fit residues: 38.1095 Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 5 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.154453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122308 restraints weight = 23205.768| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.69 r_work: 0.3071 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18926 Z= 0.103 Angle : 0.490 8.394 25882 Z= 0.243 Chirality : 0.035 0.140 3038 Planarity : 0.003 0.042 3180 Dihedral : 4.936 52.957 2656 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.23 % Allowed : 8.99 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2408 helix: 2.52 (0.14), residues: 1440 sheet: 1.26 (0.57), residues: 68 loop : -1.50 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.009 0.001 TYR D 206 PHE 0.013 0.001 PHE A 309 TRP 0.031 0.001 TRP A 452 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18924) covalent geometry : angle 0.48975 / 0.24 (25882) hydrogen bonds : bond 0.03976 / 2.64 ( 1070) hydrogen bonds : angle 3.18915 / 2.29 ( 3180) Misc. bond : bond 0.00145 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 692 ARG cc_start: 0.7494 (mtp180) cc_final: 0.6833 (mtm-85) REVERT: A 699 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8255 (tt0) REVERT: B 121 LYS cc_start: 0.8080 (tptm) cc_final: 0.7551 (tptt) REVERT: B 236 SER cc_start: 0.8678 (t) cc_final: 0.8351 (p) REVERT: B 678 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6236 (ttp80) REVERT: B 724 GLU cc_start: 0.7914 (pm20) cc_final: 0.7248 (mm-30) REVERT: C 195 HIS cc_start: 0.8126 (t-90) cc_final: 0.7534 (t70) REVERT: C 243 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 386 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8263 (mtt90) REVERT: C 452 TRP cc_start: 0.7932 (t60) cc_final: 0.7633 (t60) REVERT: C 692 ARG cc_start: 0.7470 (mtp180) cc_final: 0.6911 (mtt180) REVERT: D 452 TRP cc_start: 0.8477 (t60) cc_final: 0.8164 (t60) outliers start: 21 outliers final: 12 residues processed: 214 average time/residue: 0.1135 time to fit residues: 38.5900 Evaluate side-chains 205 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 124 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 181 optimal weight: 0.0050 chunk 205 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 637 ASN D 86 ASN D 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.151172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118825 restraints weight = 23386.698| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.66 r_work: 0.3027 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18926 Z= 0.152 Angle : 0.533 7.715 25882 Z= 0.266 Chirality : 0.038 0.165 3038 Planarity : 0.003 0.042 3180 Dihedral : 5.025 57.797 2656 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.53 % Allowed : 9.58 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.17), residues: 2408 helix: 2.54 (0.14), residues: 1428 sheet: 1.24 (0.57), residues: 68 loop : -1.54 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.012 0.001 TYR B 523 PHE 0.016 0.001 PHE B 547 TRP 0.025 0.001 TRP A 452 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (18924) covalent geometry : angle 0.53288 / 0.27 (25882) hydrogen bonds : bond 0.04972 / 3.28 ( 1070) hydrogen bonds : angle 3.26206 / 2.35 ( 3180) Misc. bond : bond 0.00195 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8505 (tptt) cc_final: 0.8173 (tptt) REVERT: A 514 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 692 ARG cc_start: 0.7555 (mtp180) cc_final: 0.6842 (mtm-85) REVERT: A 699 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8244 (tt0) REVERT: B 121 LYS cc_start: 0.8028 (tptm) cc_final: 0.7470 (tptt) REVERT: B 236 SER cc_start: 0.8706 (t) cc_final: 0.8336 (p) REVERT: B 264 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7537 (tp) REVERT: B 678 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6363 (ttp80) REVERT: B 687 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 724 GLU cc_start: 0.7923 (pm20) cc_final: 0.7187 (mm-30) REVERT: C 184 ASN cc_start: 0.7537 (m110) cc_final: 0.7275 (m110) REVERT: C 195 HIS cc_start: 0.8348 (t-90) cc_final: 0.7773 (t70) REVERT: C 692 ARG cc_start: 0.7551 (mtp180) cc_final: 0.6942 (mtt180) REVERT: D 264 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7585 (tp) REVERT: D 452 TRP cc_start: 0.8461 (t60) cc_final: 0.8125 (t60) outliers start: 26 outliers final: 15 residues processed: 206 average time/residue: 0.1239 time to fit residues: 40.5557 Evaluate side-chains 205 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 137 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 ASN D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122342 restraints weight = 23196.784| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.76 r_work: 0.3068 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18926 Z= 0.100 Angle : 0.478 7.914 25882 Z= 0.238 Chirality : 0.035 0.150 3038 Planarity : 0.003 0.042 3180 Dihedral : 4.787 58.690 2656 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.47 % Allowed : 10.16 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2408 helix: 2.77 (0.14), residues: 1436 sheet: 1.21 (0.57), residues: 68 loop : -1.43 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 615 TYR 0.010 0.001 TYR D 523 PHE 0.012 0.001 PHE C 309 TRP 0.028 0.001 TRP A 452 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (18924) covalent geometry : angle 0.47780 / 0.24 (25882) hydrogen bonds : bond 0.03835 / 2.55 ( 1070) hydrogen bonds : angle 3.15421 / 2.27 ( 3180) Misc. bond : bond 0.00103 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8611 (tptt) cc_final: 0.8344 (tptt) REVERT: A 514 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8729 (p) REVERT: A 692 ARG cc_start: 0.7541 (mtp180) cc_final: 0.6872 (mtm-85) REVERT: A 699 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8235 (tt0) REVERT: B 121 LYS cc_start: 0.8198 (tptm) cc_final: 0.7626 (tptt) REVERT: B 236 SER cc_start: 0.8682 (t) cc_final: 0.8348 (p) REVERT: B 678 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6363 (ttp80) REVERT: B 687 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7803 (pp) REVERT: B 724 GLU cc_start: 0.7926 (pm20) cc_final: 0.7191 (mm-30) REVERT: C 184 ASN cc_start: 0.7487 (m110) cc_final: 0.7255 (m110) REVERT: C 243 LEU cc_start: 0.8391 (tp) cc_final: 0.8060 (tt) REVERT: C 452 TRP cc_start: 0.7856 (t60) cc_final: 0.7602 (t60) REVERT: C 692 ARG cc_start: 0.7452 (mtp180) cc_final: 0.6890 (mtt180) REVERT: D 452 TRP cc_start: 0.8453 (t60) cc_final: 0.8145 (t60) REVERT: D 514 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.8824 (p) outliers start: 25 outliers final: 14 residues processed: 210 average time/residue: 0.1191 time to fit residues: 39.5066 Evaluate side-chains 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 196 optimal weight: 0.0000 chunk 63 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 637 ASN D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121049 restraints weight = 23220.428| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.67 r_work: 0.3066 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18926 Z= 0.113 Angle : 0.491 7.711 25882 Z= 0.243 Chirality : 0.036 0.149 3038 Planarity : 0.003 0.042 3180 Dihedral : 4.744 59.649 2656 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 10.40 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2408 helix: 2.84 (0.14), residues: 1424 sheet: 1.27 (0.58), residues: 68 loop : -1.42 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.022 0.001 TYR A 445 PHE 0.012 0.001 PHE C 309 TRP 0.031 0.001 TRP A 452 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18924) covalent geometry : angle 0.49108 / 0.24 (25882) hydrogen bonds : bond 0.04165 / 2.76 ( 1070) hydrogen bonds : angle 3.14613 / 2.27 ( 3180) Misc. bond : bond 0.00131 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 692 ARG cc_start: 0.7537 (mtp180) cc_final: 0.6854 (mtm-85) REVERT: A 699 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8172 (tt0) REVERT: B 121 LYS cc_start: 0.8144 (tptm) cc_final: 0.7542 (tptt) REVERT: B 236 SER cc_start: 0.8696 (t) cc_final: 0.8347 (p) REVERT: B 678 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6402 (ttp80) REVERT: B 687 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7811 (pp) REVERT: B 724 GLU cc_start: 0.7915 (pm20) cc_final: 0.7235 (mm-30) REVERT: C 121 LYS cc_start: 0.8675 (tptp) cc_final: 0.8341 (tptp) REVERT: C 184 ASN cc_start: 0.7547 (m110) cc_final: 0.7273 (m110) REVERT: C 243 LEU cc_start: 0.8396 (tp) cc_final: 0.8014 (tt) REVERT: C 692 ARG cc_start: 0.7465 (mtp180) cc_final: 0.6737 (mtm-85) REVERT: D 236 SER cc_start: 0.8771 (t) cc_final: 0.8312 (p) REVERT: D 452 TRP cc_start: 0.8462 (t60) cc_final: 0.8114 (t60) REVERT: D 514 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8845 (p) outliers start: 26 outliers final: 16 residues processed: 210 average time/residue: 0.1236 time to fit residues: 40.9463 Evaluate side-chains 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 9 optimal weight: 0.0170 chunk 237 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 163 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125530 restraints weight = 23171.465| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.51 r_work: 0.3120 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18926 Z= 0.091 Angle : 0.474 8.272 25882 Z= 0.233 Chirality : 0.035 0.223 3038 Planarity : 0.003 0.040 3180 Dihedral : 4.535 59.168 2656 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.12 % Allowed : 11.05 % Favored : 87.84 % 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: 2.12 (0.17), residues: 2408 helix: 2.96 (0.14), residues: 1436 sheet: 1.31 (0.58), residues: 68 loop : -1.33 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 615 TYR 0.018 0.001 TYR A 445 PHE 0.011 0.001 PHE C 309 TRP 0.032 0.001 TRP C 674 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (18924) covalent geometry : angle 0.47377 / 0.23 (25882) hydrogen bonds : bond 0.03420 / 2.28 ( 1070) hydrogen bonds : angle 3.08759 / 2.23 ( 3180) Misc. bond : bond 0.00082 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8595 (tptt) cc_final: 0.8370 (tptt) REVERT: A 243 LEU cc_start: 0.8322 (tp) cc_final: 0.8119 (tt) REVERT: A 514 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 692 ARG cc_start: 0.7515 (mtp180) cc_final: 0.6857 (mtm-85) REVERT: A 699 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8121 (tt0) REVERT: B 121 LYS cc_start: 0.8165 (tptm) cc_final: 0.7626 (tptt) REVERT: B 236 SER cc_start: 0.8667 (t) cc_final: 0.8338 (p) REVERT: B 452 TRP cc_start: 0.8459 (t60) cc_final: 0.8071 (t60) REVERT: B 514 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.8819 (p) REVERT: B 547 PHE cc_start: 0.8144 (m-80) cc_final: 0.7908 (m-80) REVERT: B 678 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6556 (mtp180) REVERT: B 687 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7771 (pp) REVERT: B 724 GLU cc_start: 0.7900 (pm20) cc_final: 0.7234 (mm-30) REVERT: C 121 LYS cc_start: 0.8611 (tptp) cc_final: 0.8293 (tptp) REVERT: C 184 ASN cc_start: 0.7562 (m110) cc_final: 0.7294 (m110) REVERT: C 243 LEU cc_start: 0.8347 (tp) cc_final: 0.8045 (tt) REVERT: C 452 TRP cc_start: 0.7826 (t60) cc_final: 0.7563 (t60) REVERT: C 692 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6750 (mtm-85) REVERT: D 236 SER cc_start: 0.8733 (t) cc_final: 0.8285 (p) REVERT: D 452 TRP cc_start: 0.8423 (t60) cc_final: 0.8093 (t60) REVERT: D 514 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.8764 (p) outliers start: 19 outliers final: 11 residues processed: 216 average time/residue: 0.1225 time to fit residues: 41.8669 Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN D 86 ASN ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.153939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121286 restraints weight = 23306.063| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.67 r_work: 0.3079 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18926 Z= 0.120 Angle : 0.505 7.496 25882 Z= 0.250 Chirality : 0.036 0.183 3038 Planarity : 0.003 0.040 3180 Dihedral : 4.598 57.739 2656 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.18 % Allowed : 11.40 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2408 helix: 2.94 (0.14), residues: 1424 sheet: 1.23 (0.58), residues: 68 loop : -1.36 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.020 0.001 TYR A 445 PHE 0.015 0.001 PHE D 545 TRP 0.032 0.001 TRP C 674 HIS 0.004 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18924) covalent geometry : angle 0.50454 / 0.25 (25882) hydrogen bonds : bond 0.04187 / 2.78 ( 1070) hydrogen bonds : angle 3.14461 / 2.27 ( 3180) Misc. bond : bond 0.00173 / 0.09 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8613 (tptt) cc_final: 0.8321 (tptt) REVERT: A 514 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 692 ARG cc_start: 0.7539 (mtp180) cc_final: 0.6796 (mtm-85) REVERT: B 121 LYS cc_start: 0.8199 (tptm) cc_final: 0.7570 (tptt) REVERT: B 236 SER cc_start: 0.8681 (t) cc_final: 0.8340 (p) REVERT: B 452 TRP cc_start: 0.8487 (t60) cc_final: 0.8074 (t60) REVERT: B 514 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.8828 (p) REVERT: B 678 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6628 (mtp180) REVERT: B 687 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7791 (pp) REVERT: B 724 GLU cc_start: 0.7850 (pm20) cc_final: 0.7218 (mm-30) REVERT: C 184 ASN cc_start: 0.7530 (m110) cc_final: 0.7259 (m110) REVERT: C 243 LEU cc_start: 0.8424 (tp) cc_final: 0.8031 (tt) REVERT: C 452 TRP cc_start: 0.7881 (t60) cc_final: 0.7595 (t60) REVERT: C 692 ARG cc_start: 0.7454 (mtp180) cc_final: 0.6735 (mtm-85) REVERT: D 236 SER cc_start: 0.8764 (t) cc_final: 0.8306 (p) REVERT: D 452 TRP cc_start: 0.8412 (t60) cc_final: 0.8025 (t60) REVERT: D 514 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.8816 (p) outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.1181 time to fit residues: 38.3188 Evaluate side-chains 208 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 132 optimal weight: 0.0170 chunk 74 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124797 restraints weight = 23207.553| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.48 r_work: 0.3105 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18926 Z= 0.100 Angle : 0.484 7.721 25882 Z= 0.240 Chirality : 0.035 0.181 3038 Planarity : 0.003 0.040 3180 Dihedral : 4.504 57.962 2656 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.06 % Allowed : 11.69 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.17), residues: 2408 helix: 2.99 (0.13), residues: 1436 sheet: 1.25 (0.58), residues: 68 loop : -1.29 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.019 0.001 TYR A 445 PHE 0.012 0.001 PHE D 545 TRP 0.031 0.001 TRP C 674 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18924) covalent geometry : angle 0.48446 / 0.24 (25882) hydrogen bonds : bond 0.03737 / 2.49 ( 1070) hydrogen bonds : angle 3.11074 / 2.24 ( 3180) Misc. bond : bond 0.00125 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.78 seconds wall clock time: 73 minutes 42.41 seconds (4422.41 seconds total)