Starting phenix.real_space_refine on Sat Sep 12 17:01:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo7_20148/09_2026/6oo7_20148.cif" } resolution = 3.8 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= 0.004 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 88 5.16 5 C 10828 2.51 5 N 2884 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16860 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4290 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 20, 'TRANS': 581} Chain breaks: 3 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 18, 'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 2, 'TRP:plan': 4, 'PHE:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 311 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4048 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 962 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 20, 'ASN:plan1': 6, 'GLU:plan': 25, 'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 5, 'PHE:plan': 8, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 408 Chain: "C" Number of atoms: 4290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4290 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 20, 'TRANS': 581} Chain breaks: 3 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 18, 'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 2, 'TRP:plan': 4, 'PHE:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 311 Chain: "D" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4048 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 962 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 20, 'ASN:plan1': 6, 'GLU:plan': 25, 'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 5, 'PHE:plan': 8, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 408 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: 3.74, per 1000 atoms: 0.22 Number of scatterers: 16860 At special positions: 0 Unit cell: (132.84, 132.84, 112.32, 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 88 16.00 O 3060 8.00 N 2884 7.00 C 10828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 764.9 milliseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 4 sheets defined 67.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.510A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.779A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.502A pdb=" N ILE A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.655A 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 366 through 372 removed outlier: 3.529A pdb=" N MET A 370 " --> pdb=" O HIS A 366 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.776A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 411 removed outlier: 3.729A pdb=" N PHE A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 457 Processing helix chain 'A' and resid 457 through 464 removed outlier: 3.577A pdb=" N ILE A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 490 removed outlier: 4.102A pdb=" N PHE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.260A pdb=" N LEU A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.544A pdb=" N GLY A 516 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 557 removed outlier: 5.667A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 603 Processing helix chain 'A' and resid 616 through 649 Processing helix chain 'A' and resid 653 through 672 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.638A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.617A 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 Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.756A 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 306 through 314 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.595A pdb=" N LEU B 324 " --> pdb=" O CYS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 366 through 372 removed outlier: 4.154A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 411 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.744A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 468 through 490 removed outlier: 3.554A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.265A pdb=" N LEU B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.575A pdb=" N ARG B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 534 Processing helix chain 'B' and resid 534 through 557 removed outlier: 3.651A pdb=" N PHE B 538 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 603 Processing helix chain 'B' and resid 617 through 634 Processing helix chain 'B' and resid 634 through 651 Processing helix chain 'B' and resid 653 through 672 removed outlier: 3.614A pdb=" N ILE B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 662 " --> pdb=" O TRP B 658 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 663 " --> pdb=" O LYS B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.501A pdb=" N ILE C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.796A pdb=" N ALA C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 306 through 314 removed outlier: 3.663A 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 366 through 372 removed outlier: 3.528A pdb=" N MET C 370 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 372 " --> pdb=" O HIS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 removed outlier: 3.750A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 411 removed outlier: 3.748A pdb=" N PHE C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 457 Processing helix chain 'C' and resid 457 through 464 removed outlier: 3.585A pdb=" N ILE C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 468 through 490 removed outlier: 4.100A pdb=" N PHE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.219A pdb=" N LEU C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.543A pdb=" N GLY C 516 " --> pdb=" O TYR C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 557 removed outlier: 5.679A pdb=" N LEU C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 603 Processing helix chain 'C' and resid 616 through 649 Processing helix chain 'C' and resid 653 through 672 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 117 through 125 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.620A pdb=" N ILE D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.643A 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 Processing helix chain 'D' and resid 246 through 254 Processing helix chain 'D' and resid 258 through 280 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.754A pdb=" N ILE D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.587A pdb=" N LEU D 324 " --> pdb=" O CYS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 366 through 372 removed outlier: 4.125A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 372 " --> pdb=" O HIS D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 411 Proline residue: D 389 - end of helix Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.765A pdb=" N ARG D 457 " --> pdb=" O TYR D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'D' and resid 468 through 490 removed outlier: 3.531A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 473 " --> pdb=" O TYR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.227A pdb=" N LEU D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.606A pdb=" N ARG D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY D 516 " --> pdb=" O TYR D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 534 Processing helix chain 'D' and resid 534 through 557 removed outlier: 3.654A pdb=" N PHE D 538 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 603 Processing helix chain 'D' and resid 617 through 634 Processing helix chain 'D' and resid 634 through 651 Processing helix chain 'D' and resid 653 through 672 removed outlier: 3.614A pdb=" N ILE D 657 " --> pdb=" O ASP D 653 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 662 " --> pdb=" O TRP D 658 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 663 " --> pdb=" O LYS D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.877A pdb=" N VAL A 338 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N CYS A 332 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 336 " --> pdb=" O CYS A 332 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 690 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 700 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR A 688 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A 702 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET A 686 " --> pdb=" O CYS A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 333 removed outlier: 6.961A pdb=" N VAL B 338 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS B 332 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 336 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP B 698 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 700 " --> pdb=" O LEU B 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 328 through 333 removed outlier: 6.894A pdb=" N VAL C 338 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N CYS C 332 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 336 " --> pdb=" O CYS C 332 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 690 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG C 700 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 688 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS C 702 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N MET C 686 " --> pdb=" O CYS C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 333 removed outlier: 6.969A pdb=" N VAL D 338 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N CYS D 332 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL D 336 " --> pdb=" O CYS D 332 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP D 698 " --> pdb=" O VAL D 689 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 700 " --> pdb=" O LEU D 687 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2792 1.29 - 1.42: 4561 1.42 - 1.56: 9719 1.56 - 1.69: 46 1.69 - 1.82: 128 Bond restraints: 17246 Sorted by residual: bond pdb=" CAJ 6EU C1001 " pdb=" OAA 6EU C1001 " ideal model delta sigma weight residual 1.439 1.769 -0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" CAJ 6EU A1001 " pdb=" OAA 6EU A1001 " ideal model delta sigma weight residual 1.439 1.769 -0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" CAJ 6EU B1001 " pdb=" OAA 6EU B1001 " ideal model delta sigma weight residual 1.439 1.751 -0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" CAJ 6EU D1001 " pdb=" OAA 6EU D1001 " ideal model delta sigma weight residual 1.439 1.750 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" CAS 6EU C1001 " pdb=" CAX 6EU C1001 " ideal model delta sigma weight residual 1.334 1.607 -0.273 2.00e-02 2.50e+03 1.87e+02 ... (remaining 17241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 22557 2.17 - 4.33: 886 4.33 - 6.50: 173 6.50 - 8.67: 71 8.67 - 10.84: 11 Bond angle restraints: 23698 Sorted by residual: angle pdb=" N GLU D 670 " pdb=" CA GLU D 670 " pdb=" C GLU D 670 " ideal model delta sigma weight residual 111.28 103.72 7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N GLU B 670 " pdb=" CA GLU B 670 " pdb=" C GLU B 670 " ideal model delta sigma weight residual 111.28 104.71 6.57 1.09e+00 8.42e-01 3.63e+01 angle pdb=" C GLN A 127 " pdb=" N ASP A 128 " pdb=" CA ASP A 128 " ideal model delta sigma weight residual 120.82 127.40 -6.58 1.50e+00 4.44e-01 1.92e+01 angle pdb=" C GLN C 127 " pdb=" N ASP C 128 " pdb=" CA ASP C 128 " ideal model delta sigma weight residual 120.82 127.39 -6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" N GLY B 208 " pdb=" CA GLY B 208 " pdb=" C GLY B 208 " ideal model delta sigma weight residual 112.37 104.97 7.40 1.84e+00 2.95e-01 1.62e+01 ... (remaining 23693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 9557 16.90 - 33.80: 309 33.80 - 50.70: 28 50.70 - 67.60: 6 67.60 - 84.50: 8 Dihedral angle restraints: 9908 sinusoidal: 2942 harmonic: 6966 Sorted by residual: dihedral pdb=" CA PHE C 197 " pdb=" C PHE C 197 " pdb=" N GLN C 198 " pdb=" CA GLN C 198 " ideal model delta harmonic sigma weight residual 180.00 149.10 30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N GLN A 198 " pdb=" CA GLN A 198 " ideal model delta harmonic sigma weight residual 180.00 149.17 30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA TYR D 159 " pdb=" C TYR D 159 " pdb=" N TYR D 160 " pdb=" CA TYR D 160 " ideal model delta harmonic sigma weight residual 180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2492 0.083 - 0.165: 262 0.165 - 0.248: 26 0.248 - 0.330: 9 0.330 - 0.413: 7 Chirality restraints: 2796 Sorted by residual: chirality pdb=" CG LEU A 621 " pdb=" CB LEU A 621 " pdb=" CD1 LEU A 621 " pdb=" CD2 LEU A 621 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CAM 6EU D1001 " pdb=" CAL 6EU D1001 " pdb=" CAP 6EU D1001 " pdb=" CAV 6EU D1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.89 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CAM 6EU B1001 " pdb=" CAL 6EU B1001 " pdb=" CAP 6EU B1001 " pdb=" CAV 6EU B1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.89 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 2793 not shown) Planarity restraints: 3044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 405 " 0.025 2.00e-02 2.50e+03 1.95e-02 6.66e+00 pdb=" CG PHE D 405 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 405 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 405 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 405 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 405 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 405 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 692 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO D 693 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 693 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 693 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 692 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO B 693 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 693 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 693 " 0.036 5.00e-02 4.00e+02 ... (remaining 3041 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4703 2.80 - 3.32: 16273 3.32 - 3.85: 26954 3.85 - 4.37: 28930 4.37 - 4.90: 50392 Nonbonded interactions: 127252 Sorted by model distance: nonbonded pdb=" O GLN C 322 " pdb=" OG SER C 325 " model vdw 2.273 3.040 nonbonded pdb=" O GLN A 322 " pdb=" OG SER A 325 " model vdw 2.279 3.040 nonbonded pdb=" O ASP C 653 " pdb=" OG SER C 656 " model vdw 2.290 3.040 nonbonded pdb=" O ASP A 653 " pdb=" OG SER A 656 " model vdw 2.291 3.040 nonbonded pdb=" O GLN B 322 " pdb=" OG SER B 325 " model vdw 2.295 3.040 ... (remaining 127247 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.080 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 0.330 17246 Z= 0.622 Angle : 1.078 10.835 23698 Z= 0.569 Chirality : 0.057 0.413 2796 Planarity : 0.007 0.064 3044 Dihedral : 9.519 84.498 5396 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 2358 helix: -0.65 (0.11), residues: 1450 sheet: -1.58 (0.41), residues: 100 loop : -1.09 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 700 TYR 0.025 0.003 TYR A 160 PHE 0.044 0.004 PHE D 405 TRP 0.032 0.003 TRP A 349 HIS 0.013 0.003 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.01283 / 0.62 (17246) covalent geometry : angle 1.07836 / 0.57 (23698) hydrogen bonds : bond 0.15346 / 10.20 ( 1111) hydrogen bonds : angle 5.98762 / 4.38 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.8636 (ttt) cc_final: 0.8264 (mmt) REVERT: A 661 GLN cc_start: 0.9562 (mm-40) cc_final: 0.9305 (mm-40) REVERT: B 268 MET cc_start: 0.8726 (tpp) cc_final: 0.8476 (mmm) REVERT: B 402 MET cc_start: 0.2595 (mmp) cc_final: 0.2271 (mmp) REVERT: C 268 MET cc_start: 0.8591 (tpp) cc_final: 0.8388 (mmm) REVERT: C 475 LEU cc_start: 0.8583 (tp) cc_final: 0.8328 (tt) REVERT: C 479 LEU cc_start: 0.9104 (tp) cc_final: 0.8898 (pp) REVERT: C 638 MET cc_start: 0.8931 (ttt) cc_final: 0.8571 (mmt) REVERT: C 661 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9291 (mm-40) REVERT: D 268 MET cc_start: 0.8741 (tpp) cc_final: 0.8472 (mmm) REVERT: D 542 TYR cc_start: 0.8620 (t80) cc_final: 0.8412 (t80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1198 time to fit residues: 50.9028 Evaluate side-chains 155 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 220 GLN A 232 HIS A 366 HIS A 485 GLN C 80 ASN C 220 GLN C 232 HIS C 366 HIS C 485 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.121962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089358 restraints weight = 58472.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091828 restraints weight = 31251.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093388 restraints weight = 21082.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094454 restraints weight = 16402.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094991 restraints weight = 13904.476| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17246 Z= 0.144 Angle : 0.594 11.139 23698 Z= 0.302 Chirality : 0.039 0.295 2796 Planarity : 0.004 0.053 3044 Dihedral : 6.549 82.135 2540 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.31 % Allowed : 5.88 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2358 helix: 1.18 (0.13), residues: 1480 sheet: -1.00 (0.48), residues: 92 loop : -0.47 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 682 TYR 0.015 0.002 TYR A 226 PHE 0.013 0.001 PHE D 317 TRP 0.021 0.001 TRP D 349 HIS 0.004 0.001 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (17246) covalent geometry : angle 0.59408 / 0.30 (23698) hydrogen bonds : bond 0.03948 / 2.61 ( 1111) hydrogen bonds : angle 4.25136 / 3.12 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 638 MET cc_start: 0.8679 (ttt) cc_final: 0.8417 (mtt) REVERT: A 686 MET cc_start: 0.7726 (tpp) cc_final: 0.7514 (tpp) REVERT: B 298 LYS cc_start: 0.9467 (mttt) cc_final: 0.9224 (mttp) REVERT: B 452 TRP cc_start: 0.7210 (t60) cc_final: 0.6858 (t60) REVERT: C 253 MET cc_start: 0.9255 (mmm) cc_final: 0.8950 (mmm) REVERT: C 447 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8751 (mm) REVERT: C 473 LEU cc_start: 0.9263 (mt) cc_final: 0.9034 (mp) REVERT: C 638 MET cc_start: 0.8800 (ttt) cc_final: 0.8538 (mmt) REVERT: D 97 LEU cc_start: 0.9559 (tp) cc_final: 0.9303 (pp) REVERT: D 298 LYS cc_start: 0.9468 (mttt) cc_final: 0.9167 (mttp) outliers start: 18 outliers final: 9 residues processed: 213 average time/residue: 0.1004 time to fit residues: 35.3699 Evaluate side-chains 176 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 165 optimal weight: 40.0000 chunk 137 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS C 485 GLN D 361 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.119731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087012 restraints weight = 59266.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089557 restraints weight = 30947.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091197 restraints weight = 20606.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092255 restraints weight = 15865.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092956 restraints weight = 13401.398| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17246 Z= 0.147 Angle : 0.590 11.890 23698 Z= 0.293 Chirality : 0.039 0.268 2796 Planarity : 0.004 0.049 3044 Dihedral : 6.139 84.249 2540 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.96 % Allowed : 6.75 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2358 helix: 1.80 (0.13), residues: 1494 sheet: 0.06 (0.55), residues: 80 loop : -0.31 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.016 0.001 TYR D 627 PHE 0.013 0.001 PHE B 317 TRP 0.017 0.001 TRP B 349 HIS 0.005 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (17246) covalent geometry : angle 0.58959 / 0.29 (23698) hydrogen bonds : bond 0.03553 / 2.33 ( 1111) hydrogen bonds : angle 3.98054 / 2.92 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 505 MET cc_start: 0.8062 (ttt) cc_final: 0.7734 (tmm) REVERT: A 638 MET cc_start: 0.8668 (ttt) cc_final: 0.8268 (mmt) REVERT: A 686 MET cc_start: 0.7785 (tpp) cc_final: 0.7541 (tpp) REVERT: B 298 LYS cc_start: 0.9497 (mttt) cc_final: 0.9196 (mttp) REVERT: B 452 TRP cc_start: 0.7310 (t60) cc_final: 0.6978 (t60) REVERT: C 402 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6296 (mmp) REVERT: C 447 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8801 (mm) REVERT: C 473 LEU cc_start: 0.9254 (mt) cc_final: 0.9045 (mt) REVERT: C 638 MET cc_start: 0.8794 (ttt) cc_final: 0.8460 (mmt) REVERT: D 298 LYS cc_start: 0.9487 (mttt) cc_final: 0.9167 (mttp) REVERT: D 402 MET cc_start: 0.2061 (tpt) cc_final: 0.1789 (tpt) REVERT: D 507 TRP cc_start: 0.4664 (m100) cc_final: 0.4434 (m100) outliers start: 27 outliers final: 17 residues processed: 185 average time/residue: 0.0987 time to fit residues: 30.4970 Evaluate side-chains 169 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 202 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 87 optimal weight: 0.0050 chunk 112 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.125415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093542 restraints weight = 57544.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096029 restraints weight = 30717.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097607 restraints weight = 20575.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098738 restraints weight = 15833.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099309 restraints weight = 13278.015| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17246 Z= 0.107 Angle : 0.533 9.975 23698 Z= 0.265 Chirality : 0.038 0.288 2796 Planarity : 0.003 0.048 3044 Dihedral : 5.868 87.493 2540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.96 % Allowed : 8.35 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.18), residues: 2358 helix: 2.01 (0.13), residues: 1512 sheet: 0.21 (0.55), residues: 80 loop : -0.24 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.019 0.001 TYR D 627 PHE 0.017 0.001 PHE A 405 TRP 0.022 0.001 TRP A 655 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (17246) covalent geometry : angle 0.53317 / 0.26 (23698) hydrogen bonds : bond 0.03142 / 2.06 ( 1111) hydrogen bonds : angle 3.72953 / 2.74 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 638 MET cc_start: 0.8572 (ttt) cc_final: 0.8219 (mmt) REVERT: B 452 TRP cc_start: 0.7220 (t60) cc_final: 0.6909 (t60) REVERT: C 447 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8835 (mm) REVERT: C 479 LEU cc_start: 0.9212 (tp) cc_final: 0.9004 (pp) REVERT: C 638 MET cc_start: 0.8825 (ttt) cc_final: 0.8445 (mmt) REVERT: D 97 LEU cc_start: 0.9427 (tp) cc_final: 0.9181 (pp) REVERT: D 298 LYS cc_start: 0.9485 (mttt) cc_final: 0.9213 (mttp) REVERT: D 402 MET cc_start: 0.2482 (tpt) cc_final: 0.2217 (tpt) REVERT: D 507 TRP cc_start: 0.4649 (m100) cc_final: 0.4298 (m100) outliers start: 27 outliers final: 15 residues processed: 193 average time/residue: 0.0973 time to fit residues: 31.8675 Evaluate side-chains 172 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 129 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 223 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.123654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090963 restraints weight = 59472.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093525 restraints weight = 30780.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095217 restraints weight = 20289.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096307 restraints weight = 15512.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096909 restraints weight = 12970.974| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17246 Z= 0.112 Angle : 0.546 10.479 23698 Z= 0.265 Chirality : 0.038 0.239 2796 Planarity : 0.003 0.048 3044 Dihedral : 5.726 88.616 2540 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.25 % Allowed : 10.01 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.18), residues: 2358 helix: 2.20 (0.13), residues: 1500 sheet: 0.38 (0.55), residues: 80 loop : -0.09 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.020 0.001 TYR D 627 PHE 0.027 0.001 PHE C 405 TRP 0.027 0.001 TRP D 384 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (17246) covalent geometry : angle 0.54626 / 0.27 (23698) hydrogen bonds : bond 0.03093 / 2.03 ( 1111) hydrogen bonds : angle 3.67721 / 2.69 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 505 MET cc_start: 0.7826 (ttt) cc_final: 0.7569 (tmm) REVERT: A 638 MET cc_start: 0.8526 (ttt) cc_final: 0.8103 (mmt) REVERT: B 452 TRP cc_start: 0.7155 (t60) cc_final: 0.6868 (t60) REVERT: C 379 LEU cc_start: 0.8776 (tp) cc_final: 0.8562 (tt) REVERT: C 447 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 479 LEU cc_start: 0.9197 (tp) cc_final: 0.8983 (pp) REVERT: C 638 MET cc_start: 0.8825 (ttt) cc_final: 0.8491 (mmt) REVERT: C 686 MET cc_start: 0.7938 (tpp) cc_final: 0.7506 (tpp) REVERT: D 97 LEU cc_start: 0.9461 (tp) cc_final: 0.9233 (pp) REVERT: D 298 LYS cc_start: 0.9495 (mttt) cc_final: 0.9227 (mttp) outliers start: 31 outliers final: 14 residues processed: 186 average time/residue: 0.0987 time to fit residues: 31.1090 Evaluate side-chains 176 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.089899 restraints weight = 58803.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092236 restraints weight = 32064.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093722 restraints weight = 21882.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094783 restraints weight = 17217.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095275 restraints weight = 14594.023| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17246 Z= 0.151 Angle : 0.595 12.163 23698 Z= 0.287 Chirality : 0.039 0.256 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.828 89.360 2540 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 11.25 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.18), residues: 2358 helix: 2.28 (0.13), residues: 1490 sheet: 0.22 (0.54), residues: 80 loop : 0.03 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.020 0.001 TYR D 627 PHE 0.030 0.001 PHE B 393 TRP 0.013 0.001 TRP C 655 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (17246) covalent geometry : angle 0.59510 / 0.29 (23698) hydrogen bonds : bond 0.03249 / 2.11 ( 1111) hydrogen bonds : angle 3.78554 / 2.78 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8849 (mm) REVERT: A 479 LEU cc_start: 0.9196 (tp) cc_final: 0.8978 (pp) REVERT: A 505 MET cc_start: 0.7776 (ttt) cc_final: 0.7473 (tmm) REVERT: A 638 MET cc_start: 0.8415 (ttt) cc_final: 0.8037 (mmt) REVERT: A 686 MET cc_start: 0.7841 (tpp) cc_final: 0.7408 (tpp) REVERT: B 452 TRP cc_start: 0.7371 (t60) cc_final: 0.7054 (t60) REVERT: C 447 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8899 (mm) REVERT: C 479 LEU cc_start: 0.9196 (tp) cc_final: 0.8959 (pp) REVERT: C 638 MET cc_start: 0.8833 (ttt) cc_final: 0.8480 (mmt) REVERT: C 686 MET cc_start: 0.7849 (tpp) cc_final: 0.7508 (tpp) REVERT: D 97 LEU cc_start: 0.9559 (tp) cc_final: 0.9295 (pp) REVERT: D 298 LYS cc_start: 0.9490 (mttt) cc_final: 0.9159 (mttp) outliers start: 29 outliers final: 18 residues processed: 175 average time/residue: 0.0950 time to fit residues: 28.5275 Evaluate side-chains 171 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 126 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 195 optimal weight: 0.0570 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN C 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.122065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.089491 restraints weight = 57379.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092011 restraints weight = 30187.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093690 restraints weight = 20104.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094648 restraints weight = 15388.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095436 restraints weight = 13068.055| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17246 Z= 0.104 Angle : 0.566 13.101 23698 Z= 0.268 Chirality : 0.038 0.249 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.623 87.745 2540 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.67 % Allowed : 12.55 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.18), residues: 2358 helix: 2.37 (0.14), residues: 1504 sheet: 0.56 (0.55), residues: 80 loop : 0.00 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.018 0.001 TYR D 627 PHE 0.032 0.001 PHE D 393 TRP 0.014 0.001 TRP C 655 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (17246) covalent geometry : angle 0.56614 / 0.27 (23698) hydrogen bonds : bond 0.02869 / 1.89 ( 1111) hydrogen bonds : angle 3.64871 / 2.68 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8716 (mm) REVERT: A 479 LEU cc_start: 0.9152 (tp) cc_final: 0.8945 (pp) REVERT: A 505 MET cc_start: 0.7715 (ttt) cc_final: 0.7462 (tmm) REVERT: A 638 MET cc_start: 0.8424 (ttt) cc_final: 0.8013 (mmt) REVERT: A 686 MET cc_start: 0.7848 (tpp) cc_final: 0.7435 (tpp) REVERT: B 452 TRP cc_start: 0.7049 (t60) cc_final: 0.6793 (t60) REVERT: C 379 LEU cc_start: 0.8767 (tp) cc_final: 0.8556 (tt) REVERT: C 447 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 479 LEU cc_start: 0.9180 (tp) cc_final: 0.8943 (pp) REVERT: C 638 MET cc_start: 0.8799 (ttt) cc_final: 0.8396 (mmt) REVERT: C 686 MET cc_start: 0.7888 (tpp) cc_final: 0.7556 (tpp) REVERT: D 97 LEU cc_start: 0.9496 (tp) cc_final: 0.9254 (pp) REVERT: D 298 LYS cc_start: 0.9492 (mttt) cc_final: 0.9218 (mttp) outliers start: 23 outliers final: 13 residues processed: 187 average time/residue: 0.0965 time to fit residues: 30.8036 Evaluate side-chains 171 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 0.0070 chunk 136 optimal weight: 6.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.120824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088977 restraints weight = 58723.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091338 restraints weight = 31526.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092957 restraints weight = 21328.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093937 restraints weight = 16550.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094709 restraints weight = 14015.350| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17246 Z= 0.139 Angle : 0.624 14.568 23698 Z= 0.293 Chirality : 0.039 0.256 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.713 88.333 2540 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.89 % Allowed : 13.35 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.18), residues: 2358 helix: 2.37 (0.13), residues: 1502 sheet: 0.42 (0.55), residues: 80 loop : 0.08 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 682 TYR 0.022 0.001 TYR D 627 PHE 0.023 0.001 PHE D 393 TRP 0.011 0.001 TRP A 221 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17246) covalent geometry : angle 0.62377 / 0.29 (23698) hydrogen bonds : bond 0.03045 / 1.99 ( 1111) hydrogen bonds : angle 3.73742 / 2.76 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 505 MET cc_start: 0.7721 (ttt) cc_final: 0.7478 (tmm) REVERT: A 638 MET cc_start: 0.8413 (ttt) cc_final: 0.8004 (mmt) REVERT: A 686 MET cc_start: 0.7942 (tpp) cc_final: 0.7579 (tpp) REVERT: B 452 TRP cc_start: 0.7007 (t60) cc_final: 0.6761 (t60) REVERT: C 387 LEU cc_start: 0.8959 (mt) cc_final: 0.8603 (tp) REVERT: C 447 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8884 (mm) REVERT: C 479 LEU cc_start: 0.9162 (tp) cc_final: 0.8909 (pp) REVERT: C 638 MET cc_start: 0.8814 (ttt) cc_final: 0.8467 (mmt) REVERT: C 686 MET cc_start: 0.7939 (tpp) cc_final: 0.7614 (tpp) REVERT: D 97 LEU cc_start: 0.9458 (tp) cc_final: 0.9253 (pp) REVERT: D 298 LYS cc_start: 0.9484 (mttt) cc_final: 0.9159 (mttp) outliers start: 26 outliers final: 18 residues processed: 170 average time/residue: 0.0948 time to fit residues: 27.5791 Evaluate side-chains 171 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 83 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 141 optimal weight: 0.0270 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.121561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090462 restraints weight = 57538.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092928 restraints weight = 30775.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.094591 restraints weight = 20523.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095479 restraints weight = 15898.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096317 restraints weight = 13502.228| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17246 Z= 0.103 Angle : 0.610 15.372 23698 Z= 0.280 Chirality : 0.039 0.275 2796 Planarity : 0.003 0.046 3044 Dihedral : 5.543 85.014 2540 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.52 % Allowed : 13.43 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.18), residues: 2358 helix: 2.44 (0.13), residues: 1502 sheet: 0.69 (0.56), residues: 80 loop : 0.10 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 682 TYR 0.023 0.001 TYR B 542 PHE 0.023 0.001 PHE D 393 TRP 0.015 0.001 TRP C 507 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (17246) covalent geometry : angle 0.60951 / 0.28 (23698) hydrogen bonds : bond 0.02819 / 1.84 ( 1111) hydrogen bonds : angle 3.64917 / 2.69 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 638 MET cc_start: 0.8404 (ttt) cc_final: 0.8030 (mmt) REVERT: A 686 MET cc_start: 0.7906 (tpp) cc_final: 0.7481 (tpp) REVERT: B 402 MET cc_start: 0.2315 (tpp) cc_final: 0.1904 (tpt) REVERT: B 507 TRP cc_start: 0.4694 (m100) cc_final: 0.4344 (m100) REVERT: C 379 LEU cc_start: 0.8756 (tp) cc_final: 0.8550 (tt) REVERT: C 387 LEU cc_start: 0.8940 (mt) cc_final: 0.8580 (tp) REVERT: C 447 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 479 LEU cc_start: 0.9160 (tp) cc_final: 0.8908 (pp) REVERT: C 638 MET cc_start: 0.8789 (ttt) cc_final: 0.8385 (mmt) REVERT: C 686 MET cc_start: 0.7957 (tpp) cc_final: 0.7580 (tpp) REVERT: D 298 LYS cc_start: 0.9468 (mttt) cc_final: 0.9193 (mttp) outliers start: 21 outliers final: 15 residues processed: 177 average time/residue: 0.0965 time to fit residues: 28.8938 Evaluate side-chains 171 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 0.6980 chunk 168 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 233 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 0.1980 chunk 154 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092283 restraints weight = 57159.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094734 restraints weight = 30560.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096381 restraints weight = 20521.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097531 restraints weight = 15775.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098040 restraints weight = 13215.042| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17246 Z= 0.096 Angle : 0.619 16.163 23698 Z= 0.280 Chirality : 0.039 0.293 2796 Planarity : 0.003 0.046 3044 Dihedral : 5.391 80.190 2540 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.94 % Allowed : 14.51 % Favored : 84.54 % 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 are not related in a simple way. whole: 2.47 (0.18), residues: 2358 helix: 2.45 (0.13), residues: 1502 sheet: 0.84 (0.56), residues: 80 loop : 0.11 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 682 TYR 0.022 0.001 TYR D 542 PHE 0.022 0.001 PHE D 393 TRP 0.013 0.001 TRP C 655 HIS 0.002 0.000 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (17246) covalent geometry : angle 0.61929 / 0.28 (23698) hydrogen bonds : bond 0.02688 / 1.76 ( 1111) hydrogen bonds : angle 3.61966 / 2.67 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.8459 (ttt) cc_final: 0.8186 (mtt) REVERT: A 686 MET cc_start: 0.7870 (tpp) cc_final: 0.7408 (tpp) REVERT: B 402 MET cc_start: 0.2329 (tpp) cc_final: 0.1957 (tpt) REVERT: B 507 TRP cc_start: 0.4536 (m100) cc_final: 0.4283 (m100) REVERT: C 379 LEU cc_start: 0.8709 (tp) cc_final: 0.8496 (tt) REVERT: C 387 LEU cc_start: 0.8940 (mt) cc_final: 0.8610 (tp) REVERT: C 447 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8781 (mm) REVERT: C 479 LEU cc_start: 0.9125 (tp) cc_final: 0.8879 (pp) REVERT: C 638 MET cc_start: 0.8785 (ttt) cc_final: 0.8458 (mmt) REVERT: C 686 MET cc_start: 0.7968 (tpp) cc_final: 0.7554 (tpp) REVERT: D 298 LYS cc_start: 0.9447 (mttt) cc_final: 0.9223 (mttp) outliers start: 13 outliers final: 10 residues processed: 175 average time/residue: 0.0931 time to fit residues: 27.9946 Evaluate side-chains 170 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 47 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 118 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 182 optimal weight: 0.0980 chunk 171 optimal weight: 30.0000 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.123286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092630 restraints weight = 57739.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095110 restraints weight = 30795.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096673 restraints weight = 20611.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097792 restraints weight = 15900.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098644 restraints weight = 13335.088| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17246 Z= 0.093 Angle : 0.618 16.308 23698 Z= 0.277 Chirality : 0.038 0.299 2796 Planarity : 0.003 0.046 3044 Dihedral : 5.190 74.889 2540 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.80 % Allowed : 14.95 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.18), residues: 2358 helix: 2.48 (0.14), residues: 1500 sheet: 0.85 (0.57), residues: 80 loop : 0.13 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 682 TYR 0.026 0.001 TYR B 542 PHE 0.022 0.001 PHE D 393 TRP 0.013 0.001 TRP C 655 HIS 0.002 0.000 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (17246) covalent geometry : angle 0.61831 / 0.28 (23698) hydrogen bonds : bond 0.02593 / 1.70 ( 1111) hydrogen bonds : angle 3.56382 / 2.62 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.32 seconds wall clock time: 47 minutes 49.95 seconds (2869.95 seconds total)