Starting phenix.real_space_refine on Sun Aug 24 09:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oo4_20145/08_2025/6oo4_20145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo4_20145/08_2025/6oo4_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_20145/08_2025/6oo4_20145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo4_20145/08_2025/6oo4_20145.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo4_20145/08_2025/6oo4_20145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo4_20145/08_2025/6oo4_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-2.0-5787/lib/python3.9/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: 5.09, per 1000 atoms: 0.28 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: 1.72 Conformation dependent library (CDL) restraints added in 884.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.59 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: 3.17 Time building geometry restraints manager: 2.28 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: 10625 14.94 - 29.89: 498 29.89 - 44.83: 92 44.83 - 59.78: 33 59.78 - 74.72: 18 Dihedral angle restraints: 11266 sinusoidal: 4134 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 11263 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: 1.640 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.540 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 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 : 10.408 74.723 6658 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 aren 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 covalent geometry : bond 0.01290 (18924) covalent geometry : angle 1.10306 (25882) hydrogen bonds : bond 0.15260 ( 1070) hydrogen bonds : angle 5.31659 ( 3180) Misc. bond : bond 0.00084 ( 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 : 0.537 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: 0.6219 (t-90) cc_final: 0.5620 (t70) REVERT: A 209 GLU cc_start: 0.6460 (mp0) cc_final: 0.6234 (mm-30) REVERT: A 221 TRP cc_start: 0.6425 (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: 0.7607 (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: 0.5421 (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: 0.5501 (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: 0.6909 (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: 0.7117 (mt-10) cc_final: 0.6576 (mm-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1724 time to fit residues: 71.5210 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 : 0.554 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3657 r_free = 0.3657 target = 0.152144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119800 restraints weight = 23455.151| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.66 r_work: 0.3038 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1401 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= 0.152 Angle : 0.598 8.543 25882 Z= 0.303 Chirality : 0.039 0.153 3038 Planarity : 0.004 0.046 3180 Dihedral : 6.387 57.981 3000 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.71 % Allowed : 4.70 % Favored : 94.59 % 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 aren not related in a simple way. whole: -0.33 (0.16), residues: 2408 helix: 0.91 (0.13), residues: 1420 sheet: 1.03 (0.55), residues: 68 loop : -2.18 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.013 0.002 TYR D 206 PHE 0.019 0.002 PHE A 309 TRP 0.012 0.001 TRP A 507 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00343 (18924) covalent geometry : angle 0.59836 (25882) hydrogen bonds : bond 0.05984 ( 1070) hydrogen bonds : angle 3.63014 ( 3180) Misc. bond : bond 0.00134 ( 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 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.8265 (t-90) cc_final: 0.7720 (t70) REVERT: A 349 TRP cc_start: 0.8998 (t60) cc_final: 0.8795 (t60) REVERT: A 526 MET cc_start: 0.8646 (mmm) cc_final: 0.8272 (mtt) REVERT: A 692 ARG cc_start: 0.7508 (mtp180) cc_final: 0.6925 (mtt90) REVERT: B 121 LYS cc_start: 0.8020 (tptm) cc_final: 0.7595 (tptt) REVERT: B 402 MET cc_start: 0.9096 (mmt) cc_final: 0.8550 (mmp) REVERT: C 135 GLN cc_start: 0.7310 (tt0) cc_final: 0.7071 (tp40) REVERT: C 195 HIS cc_start: 0.8265 (t-90) cc_final: 0.7669 (t70) REVERT: C 386 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8312 (mtt90) REVERT: C 526 MET cc_start: 0.8727 (mmm) cc_final: 0.8518 (mtt) REVERT: C 692 ARG cc_start: 0.7330 (mtp180) cc_final: 0.6743 (mtm-85) REVERT: D 236 SER cc_start: 0.8812 (t) cc_final: 0.8381 (p) REVERT: D 452 TRP cc_start: 0.8467 (t60) cc_final: 0.8167 (t60) outliers start: 12 outliers final: 11 residues processed: 209 average time/residue: 0.1362 time to fit residues: 44.4878 Evaluate side-chains 186 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 217 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122286 restraints weight = 23424.911| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.74 r_work: 0.3084 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18926 Z= 0.109 Angle : 0.518 8.946 25882 Z= 0.258 Chirality : 0.036 0.143 3038 Planarity : 0.004 0.042 3180 Dihedral : 5.770 59.898 3000 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.12 % Allowed : 6.52 % Favored : 92.36 % 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 aren not related in a simple way. whole: 0.80 (0.17), residues: 2408 helix: 1.85 (0.14), residues: 1436 sheet: 1.03 (0.55), residues: 68 loop : -1.80 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 615 TYR 0.013 0.001 TYR D 523 PHE 0.016 0.001 PHE A 309 TRP 0.014 0.001 TRP A 452 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00234 (18924) covalent geometry : angle 0.51753 (25882) hydrogen bonds : bond 0.04406 ( 1070) hydrogen bonds : angle 3.33671 ( 3180) Misc. bond : bond 0.00135 ( 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 233 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7056 (m110) cc_final: 0.6565 (m110) REVERT: A 526 MET cc_start: 0.8690 (mmm) cc_final: 0.8331 (mtt) REVERT: A 692 ARG cc_start: 0.7498 (mtp180) cc_final: 0.6833 (mtm-85) REVERT: A 699 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8245 (tt0) REVERT: B 121 LYS cc_start: 0.8043 (tptm) cc_final: 0.7616 (tptt) REVERT: B 305 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8558 (mmtp) REVERT: B 724 GLU cc_start: 0.7913 (pm20) cc_final: 0.7240 (mm-30) REVERT: C 195 HIS cc_start: 0.8201 (t-90) cc_final: 0.7620 (t70) REVERT: C 386 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8298 (mtt90) REVERT: C 452 TRP cc_start: 0.7991 (t60) cc_final: 0.7719 (t60) REVERT: C 526 MET cc_start: 0.8793 (mmm) cc_final: 0.8495 (mtt) REVERT: C 692 ARG cc_start: 0.7397 (mtp180) cc_final: 0.6778 (mtt90) REVERT: C 699 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8229 (tt0) REVERT: D 86 ASN cc_start: 0.5976 (m-40) cc_final: 0.5538 (p0) REVERT: D 236 SER cc_start: 0.8808 (t) cc_final: 0.8380 (p) REVERT: D 452 TRP cc_start: 0.8455 (t60) cc_final: 0.8156 (t60) outliers start: 19 outliers final: 9 residues processed: 222 average time/residue: 0.1262 time to fit residues: 44.5571 Evaluate side-chains 190 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 305 LYS Chi-restraints excluded: chain C residue 121 LYS 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 Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 8 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN 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 = 0.3614 r_free = 0.3614 target = 0.147957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116469 restraints weight = 23674.480| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.54 r_work: 0.2987 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.006 0.051 18926 Z= 0.229 Angle : 0.645 10.368 25882 Z= 0.321 Chirality : 0.041 0.274 3038 Planarity : 0.004 0.042 3180 Dihedral : 5.982 54.782 3000 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.82 % Allowed : 7.70 % Favored : 90.48 % 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 aren not related in a simple way. whole: 0.88 (0.17), residues: 2408 helix: 1.95 (0.14), residues: 1424 sheet: 1.22 (0.58), residues: 68 loop : -1.79 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.016 0.002 TYR B 401 PHE 0.028 0.002 PHE B 405 TRP 0.021 0.001 TRP A 452 HIS 0.008 0.002 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00563 (18924) covalent geometry : angle 0.64487 (25882) hydrogen bonds : bond 0.06481 ( 1070) hydrogen bonds : angle 3.49049 ( 3180) Misc. bond : bond 0.00847 ( 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 211 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8673 (tptt) cc_final: 0.8467 (tptt) REVERT: A 125 ASN cc_start: 0.7177 (m110) cc_final: 0.6941 (m110) REVERT: A 514 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 692 ARG cc_start: 0.7550 (mtp180) cc_final: 0.6833 (mtm-85) REVERT: A 699 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8204 (tt0) REVERT: B 121 LYS cc_start: 0.7968 (tptm) cc_final: 0.7469 (tptt) REVERT: B 724 GLU cc_start: 0.7849 (pm20) cc_final: 0.7228 (mm-30) REVERT: C 195 HIS cc_start: 0.8330 (t-90) cc_final: 0.7752 (t70) REVERT: C 386 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8613 (ttp80) REVERT: C 692 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6829 (mtm-85) REVERT: D 121 LYS cc_start: 0.8177 (tppt) cc_final: 0.7964 (tppt) REVERT: D 452 TRP cc_start: 0.8489 (t60) cc_final: 0.8134 (t60) outliers start: 31 outliers final: 20 residues processed: 199 average time/residue: 0.1274 time to fit residues: 39.3307 Evaluate side-chains 195 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 232 HIS Chi-restraints excluded: chain B residue 644 SER 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 408 VAL 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: 5.9990 chunk 202 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120445 restraints weight = 23318.525| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.63 r_work: 0.3034 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18926 Z= 0.143 Angle : 0.538 7.898 25882 Z= 0.269 Chirality : 0.037 0.229 3038 Planarity : 0.004 0.043 3180 Dihedral : 5.757 81.054 3000 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.47 % Allowed : 9.28 % Favored : 89.25 % 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 aren not related in a simple way. whole: 1.28 (0.17), residues: 2408 helix: 2.27 (0.14), residues: 1428 sheet: 1.21 (0.58), residues: 68 loop : -1.62 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.013 0.001 TYR D 206 PHE 0.015 0.001 PHE A 309 TRP 0.024 0.001 TRP A 452 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00335 (18924) covalent geometry : angle 0.53775 (25882) hydrogen bonds : bond 0.05110 ( 1070) hydrogen bonds : angle 3.33194 ( 3180) Misc. bond : bond 0.00447 ( 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 210 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8673 (tptt) cc_final: 0.8255 (tptt) REVERT: A 125 ASN cc_start: 0.7235 (m110) cc_final: 0.6952 (m110) REVERT: A 514 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8754 (p) REVERT: A 526 MET cc_start: 0.8658 (mmm) cc_final: 0.8333 (mtt) REVERT: A 692 ARG cc_start: 0.7520 (mtp180) cc_final: 0.6830 (mtm-85) REVERT: A 699 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8271 (tt0) REVERT: B 121 LYS cc_start: 0.8018 (tptm) cc_final: 0.7477 (tptt) REVERT: B 264 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7601 (tp) REVERT: B 687 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 724 GLU cc_start: 0.7899 (pm20) cc_final: 0.7196 (mm-30) REVERT: C 195 HIS cc_start: 0.8268 (t-90) cc_final: 0.7707 (t70) REVERT: C 452 TRP cc_start: 0.7833 (t60) cc_final: 0.7538 (t60) REVERT: C 692 ARG cc_start: 0.7514 (mtp180) cc_final: 0.6917 (mtt180) REVERT: D 121 LYS cc_start: 0.8100 (tppt) cc_final: 0.7819 (tppt) REVERT: D 264 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7581 (tp) REVERT: D 452 TRP cc_start: 0.8476 (t60) cc_final: 0.8078 (t60) outliers start: 25 outliers final: 16 residues processed: 203 average time/residue: 0.1104 time to fit residues: 35.5384 Evaluate side-chains 197 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 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 264 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 124 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3661 r_free = 0.3661 target = 0.152190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119710 restraints weight = 23304.738| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.68 r_work: 0.3045 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18926 Z= 0.124 Angle : 0.511 7.924 25882 Z= 0.255 Chirality : 0.037 0.211 3038 Planarity : 0.003 0.043 3180 Dihedral : 5.555 89.944 3000 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.41 % Allowed : 9.64 % Favored : 88.95 % 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 aren not related in a simple way. whole: 1.56 (0.17), residues: 2408 helix: 2.51 (0.14), residues: 1428 sheet: 1.25 (0.58), residues: 68 loop : -1.54 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 386 TYR 0.013 0.001 TYR C 469 PHE 0.014 0.001 PHE A 309 TRP 0.028 0.001 TRP A 452 HIS 0.004 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00283 (18924) covalent geometry : angle 0.51101 (25882) hydrogen bonds : bond 0.04543 ( 1070) hydrogen bonds : angle 3.25136 ( 3180) Misc. bond : bond 0.00312 ( 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 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8811 (tptt) cc_final: 0.8349 (tptt) REVERT: A 125 ASN cc_start: 0.7307 (m110) cc_final: 0.6980 (m110) REVERT: A 514 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8704 (p) REVERT: A 526 MET cc_start: 0.8739 (mmm) cc_final: 0.8349 (mtt) REVERT: A 692 ARG cc_start: 0.7552 (mtp180) cc_final: 0.6866 (mtm-85) REVERT: A 699 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8246 (tt0) REVERT: B 121 LYS cc_start: 0.8158 (tptm) cc_final: 0.7583 (tptt) REVERT: B 264 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7539 (tp) REVERT: B 687 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7700 (pp) REVERT: B 724 GLU cc_start: 0.7937 (pm20) cc_final: 0.7182 (mm-30) REVERT: C 195 HIS cc_start: 0.8288 (t-90) cc_final: 0.7726 (t70) REVERT: C 243 LEU cc_start: 0.8426 (tp) cc_final: 0.8022 (tt) REVERT: C 692 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6954 (mtt180) REVERT: D 452 TRP cc_start: 0.8463 (t60) cc_final: 0.8129 (t60) outliers start: 24 outliers final: 15 residues processed: 209 average time/residue: 0.1080 time to fit residues: 35.5669 Evaluate side-chains 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 687 LEU Chi-restraints excluded: chain B residue 699 GLU 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 644 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 0.0470 chunk 141 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN B 637 ASN D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.154431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121681 restraints weight = 23245.304| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3080 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2670 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= 0.102 Angle : 0.492 10.645 25882 Z= 0.242 Chirality : 0.036 0.158 3038 Planarity : 0.003 0.043 3180 Dihedral : 5.145 48.656 3000 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.12 % Allowed : 11.10 % Favored : 87.78 % 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 aren not related in a simple way. whole: 1.84 (0.17), residues: 2408 helix: 2.71 (0.14), residues: 1440 sheet: 1.27 (0.58), residues: 68 loop : -1.41 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 386 TYR 0.014 0.001 TYR C 469 PHE 0.012 0.001 PHE C 309 TRP 0.032 0.001 TRP A 452 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00220 (18924) covalent geometry : angle 0.49210 (25882) hydrogen bonds : bond 0.03898 ( 1070) hydrogen bonds : angle 3.15434 ( 3180) Misc. bond : bond 0.00494 ( 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 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8836 (tptt) cc_final: 0.8347 (tptt) REVERT: A 125 ASN cc_start: 0.7277 (m110) cc_final: 0.6935 (m110) REVERT: A 514 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 526 MET cc_start: 0.8715 (mmm) cc_final: 0.8340 (mtt) REVERT: A 692 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6872 (mtm-85) REVERT: A 699 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8247 (tt0) REVERT: B 121 LYS cc_start: 0.8176 (tptm) cc_final: 0.7608 (tptt) REVERT: B 236 SER cc_start: 0.8687 (t) cc_final: 0.8345 (p) REVERT: B 687 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 724 GLU cc_start: 0.7933 (pm20) cc_final: 0.7240 (mm-30) REVERT: C 243 LEU cc_start: 0.8412 (tp) cc_final: 0.8034 (tt) REVERT: C 452 TRP cc_start: 0.7823 (t60) cc_final: 0.7539 (t60) REVERT: C 692 ARG cc_start: 0.7484 (mtp180) cc_final: 0.6882 (mtt180) REVERT: D 236 SER cc_start: 0.8777 (t) cc_final: 0.8343 (p) REVERT: D 452 TRP cc_start: 0.8492 (t60) cc_final: 0.8184 (t60) outliers start: 19 outliers final: 9 residues processed: 218 average time/residue: 0.1096 time to fit residues: 37.8176 Evaluate side-chains 205 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 687 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 146 optimal weight: 0.0270 chunk 220 optimal weight: 7.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 637 ASN D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118991 restraints weight = 23319.997| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.68 r_work: 0.3028 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18926 Z= 0.149 Angle : 0.538 7.660 25882 Z= 0.266 Chirality : 0.037 0.216 3038 Planarity : 0.003 0.042 3180 Dihedral : 5.376 71.549 3000 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.29 % Allowed : 10.87 % 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 aren not related in a simple way. whole: 1.73 (0.17), residues: 2408 helix: 2.65 (0.14), residues: 1428 sheet: 1.28 (0.58), residues: 68 loop : -1.46 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 615 TYR 0.022 0.001 TYR A 445 PHE 0.016 0.001 PHE B 547 TRP 0.030 0.001 TRP A 452 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00354 (18924) covalent geometry : angle 0.53823 (25882) hydrogen bonds : bond 0.04852 ( 1070) hydrogen bonds : angle 3.22477 ( 3180) Misc. bond : bond 0.00286 ( 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 210 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8864 (tptt) cc_final: 0.8335 (tptt) REVERT: A 125 ASN cc_start: 0.7329 (m110) cc_final: 0.6941 (m110) REVERT: A 526 MET cc_start: 0.8773 (mmm) cc_final: 0.8400 (mtt) REVERT: A 692 ARG cc_start: 0.7600 (mtp180) cc_final: 0.6837 (mtm-85) REVERT: A 699 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8231 (tt0) REVERT: B 121 LYS cc_start: 0.8149 (tptm) cc_final: 0.7573 (tptt) REVERT: B 236 SER cc_start: 0.8667 (t) cc_final: 0.8294 (p) REVERT: B 264 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7626 (tp) REVERT: B 724 GLU cc_start: 0.7915 (pm20) cc_final: 0.7242 (mm-30) REVERT: C 184 ASN cc_start: 0.7582 (m110) cc_final: 0.7322 (m110) REVERT: C 243 LEU cc_start: 0.8489 (tp) cc_final: 0.8107 (tt) REVERT: C 692 ARG cc_start: 0.7525 (mtp180) cc_final: 0.6911 (mtt180) REVERT: D 236 SER cc_start: 0.8800 (t) cc_final: 0.8383 (p) REVERT: D 452 TRP cc_start: 0.8507 (t60) cc_final: 0.8185 (t60) REVERT: D 687 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7717 (pp) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.1225 time to fit residues: 39.4453 Evaluate side-chains 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 555 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 264 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 640 ILE Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 9 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123764 restraints weight = 23222.495| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.65 r_work: 0.3081 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2828 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= 0.104 Angle : 0.500 10.661 25882 Z= 0.247 Chirality : 0.036 0.165 3038 Planarity : 0.003 0.045 3180 Dihedral : 4.982 48.184 3000 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 11.46 % Favored : 87.60 % 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 aren not related in a simple way. whole: 1.85 (0.17), residues: 2408 helix: 2.66 (0.14), residues: 1464 sheet: 1.28 (0.57), residues: 68 loop : -1.40 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 615 TYR 0.019 0.001 TYR A 445 PHE 0.011 0.001 PHE C 309 TRP 0.033 0.001 TRP C 674 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00224 (18924) covalent geometry : angle 0.50003 (25882) hydrogen bonds : bond 0.03909 ( 1070) hydrogen bonds : angle 3.16922 ( 3180) Misc. bond : bond 0.00519 ( 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 214 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8854 (tptt) cc_final: 0.8432 (tptt) REVERT: A 125 ASN cc_start: 0.7328 (m110) cc_final: 0.6950 (m110) REVERT: A 526 MET cc_start: 0.8724 (mmm) cc_final: 0.8303 (mtt) REVERT: A 692 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6813 (mtm-85) REVERT: A 699 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8184 (tt0) REVERT: B 121 LYS cc_start: 0.8220 (tptm) cc_final: 0.7612 (tptt) REVERT: B 236 SER cc_start: 0.8639 (t) cc_final: 0.8276 (p) REVERT: B 452 TRP cc_start: 0.8480 (t60) cc_final: 0.8059 (t60) REVERT: B 724 GLU cc_start: 0.7870 (pm20) cc_final: 0.7224 (mm-30) REVERT: C 104 LEU cc_start: 0.8034 (mt) cc_final: 0.7829 (mt) REVERT: C 184 ASN cc_start: 0.7490 (m110) cc_final: 0.7238 (m110) REVERT: C 243 LEU cc_start: 0.8435 (tp) cc_final: 0.8056 (tt) REVERT: C 402 MET cc_start: 0.8706 (mmt) cc_final: 0.8296 (mmt) REVERT: C 452 TRP cc_start: 0.7800 (t60) cc_final: 0.7538 (t60) REVERT: C 692 ARG cc_start: 0.7490 (mtp180) cc_final: 0.6743 (mtm-85) REVERT: D 236 SER cc_start: 0.8756 (t) cc_final: 0.8312 (p) REVERT: D 452 TRP cc_start: 0.8472 (t60) cc_final: 0.8165 (t60) REVERT: D 687 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7699 (pp) outliers start: 16 outliers final: 11 residues processed: 206 average time/residue: 0.1148 time to fit residues: 37.7010 Evaluate side-chains 208 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER 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 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 637 ASN D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118094 restraints weight = 23436.394| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.64 r_work: 0.3020 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18926 Z= 0.173 Angle : 0.569 9.148 25882 Z= 0.282 Chirality : 0.038 0.159 3038 Planarity : 0.004 0.053 3180 Dihedral : 5.227 53.258 3000 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.12 % Allowed : 11.34 % Favored : 87.54 % 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 aren not related in a simple way. whole: 1.72 (0.17), residues: 2408 helix: 2.64 (0.14), residues: 1428 sheet: 1.29 (0.57), residues: 68 loop : -1.46 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 615 TYR 0.021 0.002 TYR A 445 PHE 0.018 0.001 PHE B 547 TRP 0.032 0.001 TRP C 674 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00419 (18924) covalent geometry : angle 0.56875 (25882) hydrogen bonds : bond 0.05306 ( 1070) hydrogen bonds : angle 3.28259 ( 3180) Misc. bond : bond 0.00636 ( 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 210 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8871 (tptt) cc_final: 0.8418 (tptt) REVERT: A 125 ASN cc_start: 0.7352 (m110) cc_final: 0.6903 (m110) REVERT: A 692 ARG cc_start: 0.7596 (mtp180) cc_final: 0.6945 (mtm-85) REVERT: B 121 LYS cc_start: 0.8234 (tptm) cc_final: 0.7623 (tptt) REVERT: B 236 SER cc_start: 0.8692 (t) cc_final: 0.8288 (p) REVERT: B 452 TRP cc_start: 0.8501 (t60) cc_final: 0.8068 (t60) REVERT: B 687 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7877 (pp) REVERT: B 724 GLU cc_start: 0.7888 (pm20) cc_final: 0.7229 (mm-30) REVERT: C 184 ASN cc_start: 0.7558 (m110) cc_final: 0.7302 (m110) REVERT: C 692 ARG cc_start: 0.7500 (mtp180) cc_final: 0.6842 (mtt180) REVERT: D 452 TRP cc_start: 0.8492 (t60) cc_final: 0.8129 (t60) REVERT: D 687 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7772 (pp) outliers start: 19 outliers final: 15 residues processed: 204 average time/residue: 0.1278 time to fit residues: 41.2730 Evaluate side-chains 200 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 555 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER 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 C residue 637 ASN 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 640 ILE Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118017 restraints weight = 23380.127| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.73 r_work: 0.3016 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 18926 Z= 0.155 Angle : 0.731 59.198 25882 Z= 0.412 Chirality : 0.039 0.642 3038 Planarity : 0.004 0.071 3180 Dihedral : 5.255 53.191 3000 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.23 % Allowed : 11.57 % Favored : 87.19 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: 1.73 (0.17), residues: 2408 helix: 2.65 (0.14), residues: 1428 sheet: 1.29 (0.57), residues: 68 loop : -1.45 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 615 TYR 0.021 0.001 TYR A 445 PHE 0.018 0.001 PHE B 547 TRP 0.030 0.001 TRP C 674 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00330 (18924) covalent geometry : angle 0.73064 (25882) hydrogen bonds : bond 0.05149 ( 1070) hydrogen bonds : angle 3.29403 ( 3180) Misc. bond : bond 0.00563 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.07 seconds wall clock time: 73 minutes 51.27 seconds (4431.27 seconds total)