Starting phenix.real_space_refine on Wed Mar 4 23:08:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oo7_20148/03_2026/6oo7_20148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo7_20148/03_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_20148/03_2026/6oo7_20148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo7_20148/03_2026/6oo7_20148.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo7_20148/03_2026/6oo7_20148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo7_20148/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.79, 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: 1.63 Conformation dependent library (CDL) restraints added in 815.8 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: 0.52 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: 2.59 Time building geometry restraints manager: 2.17 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: 9848 16.90 - 33.80: 336 33.80 - 50.70: 38 50.70 - 67.60: 22 67.60 - 84.50: 8 Dihedral angle restraints: 10252 sinusoidal: 3286 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 10249 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: 0.03 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: 1.600 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 10.199 84.498 5740 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 covalent geometry : bond 0.01283 (17246) covalent geometry : angle 1.07836 (23698) hydrogen bonds : bond 0.15346 ( 1111) hydrogen bonds : angle 5.98762 ( 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 : 0.584 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: 0.1178 time to fit residues: 49.6155 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 : 0.627 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3987 r_free = 0.3987 target = 0.120323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087238 restraints weight = 58762.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089777 restraints weight = 31109.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091468 restraints weight = 20859.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092441 restraints weight = 16053.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093208 restraints weight = 13648.338| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17246 Z= 0.144 Angle : 0.597 11.291 23698 Z= 0.304 Chirality : 0.039 0.298 2796 Planarity : 0.004 0.052 3044 Dihedral : 6.940 81.446 2884 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.38 % Allowed : 5.73 % Favored : 92.89 % 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: 0.75 (0.17), residues: 2358 helix: 1.17 (0.13), residues: 1480 sheet: -0.94 (0.45), residues: 100 loop : -0.48 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 682 TYR 0.015 0.002 TYR A 226 PHE 0.012 0.001 PHE D 205 TRP 0.022 0.001 TRP B 349 HIS 0.004 0.001 HIS D 167 Details of bonding type rmsd covalent geometry : bond 0.00298 (17246) covalent geometry : angle 0.59728 (23698) hydrogen bonds : bond 0.03956 ( 1111) hydrogen bonds : angle 4.27175 ( 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 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 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: 0.9042 (OUTLIER) cc_final: 0.8830 (mm) REVERT: A 638 MET cc_start: 0.8701 (ttt) cc_final: 0.8434 (mtt) REVERT: A 686 MET cc_start: 0.7728 (tpp) cc_final: 0.7516 (tpp) REVERT: B 298 LYS cc_start: 0.9476 (mttt) cc_final: 0.9229 (mttp) REVERT: B 452 TRP cc_start: 0.7164 (t60) cc_final: 0.6812 (t60) REVERT: C 253 MET cc_start: 0.9299 (mmm) cc_final: 0.8992 (mmm) REVERT: C 447 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8760 (mm) REVERT: C 473 LEU cc_start: 0.9248 (mt) cc_final: 0.9009 (mp) REVERT: C 638 MET cc_start: 0.8785 (ttt) cc_final: 0.8531 (mmt) REVERT: D 97 LEU cc_start: 0.9541 (tp) cc_final: 0.9283 (pp) REVERT: D 298 LYS cc_start: 0.9467 (mttt) cc_final: 0.9158 (mttp) outliers start: 19 outliers final: 10 residues processed: 211 average time/residue: 0.1049 time to fit residues: 36.2170 Evaluate side-chains 175 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 165 optimal weight: 40.0000 chunk 137 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.116163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083043 restraints weight = 60512.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.085485 restraints weight = 31810.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087050 restraints weight = 21271.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088104 restraints weight = 16386.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088757 restraints weight = 13836.021| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17246 Z= 0.259 Angle : 0.714 11.690 23698 Z= 0.357 Chirality : 0.041 0.259 2796 Planarity : 0.004 0.050 3044 Dihedral : 6.807 82.607 2884 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.96 % Allowed : 7.33 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2358 helix: 1.42 (0.13), residues: 1496 sheet: -0.78 (0.47), residues: 100 loop : -0.43 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 682 TYR 0.019 0.002 TYR A 226 PHE 0.020 0.002 PHE D 317 TRP 0.023 0.002 TRP D 349 HIS 0.008 0.002 HIS D 167 Details of bonding type rmsd covalent geometry : bond 0.00562 (17246) covalent geometry : angle 0.71386 (23698) hydrogen bonds : bond 0.04303 ( 1111) hydrogen bonds : angle 4.34582 ( 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 192 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8850 (mm) REVERT: A 505 MET cc_start: 0.8116 (ttt) cc_final: 0.7808 (tmm) REVERT: A 638 MET cc_start: 0.8703 (ttt) cc_final: 0.8455 (mtt) REVERT: A 686 MET cc_start: 0.7766 (tpp) cc_final: 0.7549 (tpp) REVERT: B 298 LYS cc_start: 0.9498 (mttt) cc_final: 0.9247 (mttp) REVERT: B 452 TRP cc_start: 0.7429 (t60) cc_final: 0.7083 (t60) REVERT: C 402 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6387 (mmp) REVERT: C 447 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8854 (mm) REVERT: C 638 MET cc_start: 0.8812 (ttt) cc_final: 0.8442 (mmt) REVERT: D 298 LYS cc_start: 0.9490 (mttt) cc_final: 0.9231 (mttp) REVERT: D 402 MET cc_start: 0.2346 (tpt) cc_final: 0.2056 (tpt) REVERT: D 505 MET cc_start: 0.5784 (ttp) cc_final: 0.5574 (tpp) REVERT: D 507 TRP cc_start: 0.4838 (m100) cc_final: 0.4596 (m100) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.0952 time to fit residues: 28.5261 Evaluate side-chains 176 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 224 VAL 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 308 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 131 ASN 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 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 361 HIS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 387 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: 2.9990 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS B 361 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086919 restraints weight = 58506.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089440 restraints weight = 31352.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091110 restraints weight = 21034.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092069 restraints weight = 16180.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092827 restraints weight = 13763.072| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17246 Z= 0.153 Angle : 0.580 9.756 23698 Z= 0.291 Chirality : 0.039 0.276 2796 Planarity : 0.004 0.048 3044 Dihedral : 6.430 85.320 2884 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.32 % Allowed : 9.36 % Favored : 88.32 % 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: 1.57 (0.18), residues: 2358 helix: 1.85 (0.13), residues: 1494 sheet: -0.66 (0.52), residues: 92 loop : -0.30 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.017 0.001 TYR D 627 PHE 0.019 0.001 PHE A 405 TRP 0.020 0.001 TRP A 655 HIS 0.010 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00330 (17246) covalent geometry : angle 0.57971 (23698) hydrogen bonds : bond 0.03573 ( 1111) hydrogen bonds : angle 4.01359 ( 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 192 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.694 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: 0.9123 (OUTLIER) cc_final: 0.8854 (mm) REVERT: A 638 MET cc_start: 0.8535 (ttt) cc_final: 0.8169 (mmt) REVERT: B 298 LYS cc_start: 0.9525 (mttt) cc_final: 0.9244 (mttp) REVERT: B 402 MET cc_start: 0.2560 (mmp) cc_final: 0.2245 (mmt) REVERT: B 452 TRP cc_start: 0.7360 (t60) cc_final: 0.7014 (t60) REVERT: C 479 LEU cc_start: 0.9212 (tp) cc_final: 0.9011 (pp) REVERT: C 638 MET cc_start: 0.8836 (ttt) cc_final: 0.8488 (mmt) REVERT: D 97 LEU cc_start: 0.9491 (tp) cc_final: 0.9223 (pp) REVERT: D 402 MET cc_start: 0.2310 (OUTLIER) cc_final: 0.1962 (tpt) REVERT: D 505 MET cc_start: 0.6066 (ttp) cc_final: 0.5841 (tpp) REVERT: D 507 TRP cc_start: 0.4670 (m100) cc_final: 0.4372 (m100) outliers start: 32 outliers final: 21 residues processed: 178 average time/residue: 0.0952 time to fit residues: 28.9037 Evaluate side-chains 169 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 150 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 361 HIS 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 465 PHE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 361 HIS Chi-restraints excluded: chain D residue 402 MET 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: 2.9990 chunk 117 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN B 361 HIS C 131 ASN 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 = 0.119578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.086728 restraints weight = 58646.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089261 restraints weight = 30769.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090893 restraints weight = 20500.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091860 restraints weight = 15772.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092640 restraints weight = 13348.029| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17246 Z= 0.110 Angle : 0.550 11.565 23698 Z= 0.271 Chirality : 0.038 0.306 2796 Planarity : 0.004 0.063 3044 Dihedral : 6.191 88.630 2884 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.96 % Allowed : 10.81 % Favored : 87.23 % 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: 1.89 (0.18), residues: 2358 helix: 2.08 (0.13), residues: 1498 sheet: 0.19 (0.56), residues: 80 loop : -0.23 (0.24), residues: 780 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 0.018 0.001 TRP A 655 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00226 (17246) covalent geometry : angle 0.55048 (23698) hydrogen bonds : bond 0.03192 ( 1111) hydrogen bonds : angle 3.83233 ( 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 190 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.549 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: symmetry clash REVERT: A 447 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 505 MET cc_start: 0.7868 (ttt) cc_final: 0.7598 (tmm) REVERT: A 638 MET cc_start: 0.8548 (ttt) cc_final: 0.8180 (mmt) REVERT: B 298 LYS cc_start: 0.9510 (mttt) cc_final: 0.9176 (mttp) REVERT: B 402 MET cc_start: 0.2645 (mmp) cc_final: 0.2338 (mmt) REVERT: B 452 TRP cc_start: 0.7386 (t60) cc_final: 0.7054 (t60) REVERT: C 268 MET cc_start: 0.8709 (tpp) cc_final: 0.8502 (mmm) REVERT: C 402 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6277 (mmp) REVERT: C 479 LEU cc_start: 0.9194 (tp) cc_final: 0.8973 (pp) REVERT: C 638 MET cc_start: 0.8832 (ttt) cc_final: 0.8441 (mmt) REVERT: C 686 MET cc_start: 0.7986 (tpp) cc_final: 0.7510 (tpp) REVERT: D 97 LEU cc_start: 0.9519 (tp) cc_final: 0.9268 (pp) outliers start: 27 outliers final: 15 residues processed: 184 average time/residue: 0.0978 time to fit residues: 30.3444 Evaluate side-chains 167 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU 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 343 LEU Chi-restraints excluded: chain B residue 361 HIS 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 402 MET Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 361 HIS 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: 5.9990 chunk 51 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 201 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 31 optimal weight: 0.0070 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.123870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091621 restraints weight = 58141.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094053 restraints weight = 31181.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095722 restraints weight = 20963.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096794 restraints weight = 16114.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097360 restraints weight = 13547.515| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17246 Z= 0.134 Angle : 0.570 12.806 23698 Z= 0.279 Chirality : 0.039 0.303 2796 Planarity : 0.003 0.048 3044 Dihedral : 6.088 89.467 2884 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.96 % Allowed : 11.47 % Favored : 86.57 % 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: 2.01 (0.18), residues: 2358 helix: 2.16 (0.13), residues: 1504 sheet: 0.25 (0.56), residues: 80 loop : -0.18 (0.24), residues: 774 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 0.016 0.001 PHE C 405 TRP 0.027 0.001 TRP D 384 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00294 (17246) covalent geometry : angle 0.57042 (23698) hydrogen bonds : bond 0.03178 ( 1111) hydrogen bonds : angle 3.81749 ( 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 183 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.530 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: 0.9112 (OUTLIER) cc_final: 0.8838 (mm) REVERT: A 638 MET cc_start: 0.8422 (ttt) cc_final: 0.8093 (mmt) REVERT: A 686 MET cc_start: 0.7718 (tpp) cc_final: 0.7260 (tpp) REVERT: B 298 LYS cc_start: 0.9477 (mttt) cc_final: 0.9145 (mttp) REVERT: B 402 MET cc_start: 0.2752 (mmp) cc_final: 0.2422 (mmt) REVERT: B 452 TRP cc_start: 0.7302 (t60) cc_final: 0.6998 (t60) REVERT: C 268 MET cc_start: 0.8552 (tpp) cc_final: 0.8352 (mmm) REVERT: C 379 LEU cc_start: 0.8815 (tp) cc_final: 0.8591 (tt) REVERT: C 479 LEU cc_start: 0.9189 (tp) cc_final: 0.8986 (pp) REVERT: C 638 MET cc_start: 0.8835 (ttt) cc_final: 0.8435 (mmt) REVERT: C 686 MET cc_start: 0.7959 (tpp) cc_final: 0.7545 (tpp) REVERT: D 97 LEU cc_start: 0.9435 (tp) cc_final: 0.9209 (pp) REVERT: D 505 MET cc_start: 0.5560 (tpp) cc_final: 0.5110 (tpp) outliers start: 27 outliers final: 21 residues processed: 173 average time/residue: 0.0970 time to fit residues: 28.5212 Evaluate side-chains 168 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 308 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 247 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 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 361 HIS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 452 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 126 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 67 optimal weight: 0.0000 chunk 38 optimal weight: 6.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN B 361 HIS C 366 HIS C 485 GLN D 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.121209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088085 restraints weight = 58421.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.090567 restraints weight = 30716.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092166 restraints weight = 20554.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093154 restraints weight = 15954.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093705 restraints weight = 13611.419| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17246 Z= 0.098 Angle : 0.564 14.773 23698 Z= 0.268 Chirality : 0.039 0.299 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.881 89.582 2884 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 12.48 % Favored : 85.63 % 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: 2.26 (0.18), residues: 2358 helix: 2.33 (0.13), residues: 1492 sheet: 0.47 (0.56), residues: 80 loop : 0.01 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 173 TYR 0.022 0.001 TYR D 627 PHE 0.019 0.001 PHE A 405 TRP 0.014 0.001 TRP A 655 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00205 (17246) covalent geometry : angle 0.56400 (23698) hydrogen bonds : bond 0.02961 ( 1111) hydrogen bonds : angle 3.69335 ( 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 194 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 TYR cc_start: 0.8825 (t80) cc_final: 0.8607 (t80) REVERT: A 447 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8848 (mm) REVERT: A 479 LEU cc_start: 0.9149 (tp) cc_final: 0.8948 (pp) REVERT: A 638 MET cc_start: 0.8451 (ttt) cc_final: 0.8100 (mmt) REVERT: A 686 MET cc_start: 0.7805 (tpp) cc_final: 0.7415 (tpp) REVERT: B 298 LYS cc_start: 0.9502 (mttt) cc_final: 0.9164 (mttp) REVERT: B 402 MET cc_start: 0.2603 (mmp) cc_final: 0.2262 (mmt) REVERT: B 452 TRP cc_start: 0.7376 (t60) cc_final: 0.7067 (t60) REVERT: B 686 MET cc_start: 0.9368 (mmt) cc_final: 0.9036 (mmm) REVERT: C 226 TYR cc_start: 0.8854 (t80) cc_final: 0.8616 (t80) REVERT: C 379 LEU cc_start: 0.8747 (tp) cc_final: 0.8541 (tt) REVERT: C 479 LEU cc_start: 0.9197 (tp) cc_final: 0.8946 (pp) REVERT: C 638 MET cc_start: 0.8827 (ttt) cc_final: 0.8464 (mmt) REVERT: C 686 MET cc_start: 0.8016 (tpp) cc_final: 0.7646 (tpp) REVERT: D 97 LEU cc_start: 0.9599 (tp) cc_final: 0.9325 (pp) REVERT: D 387 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7672 (pp) REVERT: D 505 MET cc_start: 0.5457 (tpp) cc_final: 0.4991 (tpp) outliers start: 26 outliers final: 18 residues processed: 189 average time/residue: 0.0953 time to fit residues: 30.6689 Evaluate side-chains 172 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 343 LEU Chi-restraints excluded: chain B residue 361 HIS 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 400 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 361 HIS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 387 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: 2.9990 chunk 25 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS B 361 HIS D 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090747 restraints weight = 58154.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093070 restraints weight = 31641.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094524 restraints weight = 21402.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.095660 restraints weight = 16629.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096231 restraints weight = 14125.203| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17246 Z= 0.159 Angle : 0.606 14.916 23698 Z= 0.291 Chirality : 0.040 0.299 2796 Planarity : 0.004 0.047 3044 Dihedral : 5.889 88.838 2884 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.96 % Allowed : 13.93 % Favored : 84.11 % 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: 2.25 (0.18), residues: 2358 helix: 2.33 (0.13), residues: 1490 sheet: 0.31 (0.56), residues: 80 loop : 0.01 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.024 0.001 TYR D 627 PHE 0.024 0.001 PHE A 405 TRP 0.011 0.001 TRP A 655 HIS 0.007 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00352 (17246) covalent geometry : angle 0.60639 (23698) hydrogen bonds : bond 0.03188 ( 1111) hydrogen bonds : angle 3.83181 ( 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 177 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 479 LEU cc_start: 0.9145 (tp) cc_final: 0.8941 (pp) REVERT: A 638 MET cc_start: 0.8434 (ttt) cc_final: 0.8090 (mmt) REVERT: A 686 MET cc_start: 0.7812 (tpp) cc_final: 0.7432 (tpp) REVERT: B 298 LYS cc_start: 0.9509 (mttt) cc_final: 0.9173 (mttp) REVERT: B 402 MET cc_start: 0.3031 (mmp) cc_final: 0.2660 (mmt) REVERT: B 452 TRP cc_start: 0.7260 (t60) cc_final: 0.7003 (t60) REVERT: C 479 LEU cc_start: 0.9218 (tp) cc_final: 0.8956 (pp) REVERT: C 638 MET cc_start: 0.8837 (ttt) cc_final: 0.8470 (mmt) REVERT: C 686 MET cc_start: 0.7956 (tpp) cc_final: 0.7606 (tpp) REVERT: D 97 LEU cc_start: 0.9467 (tp) cc_final: 0.9250 (pp) REVERT: D 387 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7617 (pp) outliers start: 27 outliers final: 21 residues processed: 168 average time/residue: 0.0942 time to fit residues: 26.9680 Evaluate side-chains 170 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 343 LEU Chi-restraints excluded: chain B residue 361 HIS 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 451 LEU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 361 HIS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 387 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: 0.7980 chunk 231 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN B 361 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 = 0.4000 r_free = 0.4000 target = 0.124118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092110 restraints weight = 57470.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094494 restraints weight = 30906.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.096145 restraints weight = 20848.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097120 restraints weight = 16091.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097853 restraints weight = 13629.893| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17246 Z= 0.109 Angle : 0.588 15.699 23698 Z= 0.276 Chirality : 0.039 0.289 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.740 89.518 2884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.52 % Allowed : 14.80 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.18), residues: 2358 helix: 2.40 (0.13), residues: 1488 sheet: 0.48 (0.56), residues: 80 loop : 0.08 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.021 0.001 TYR D 627 PHE 0.019 0.001 PHE C 405 TRP 0.012 0.001 TRP A 655 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00235 (17246) covalent geometry : angle 0.58761 (23698) hydrogen bonds : bond 0.02977 ( 1111) hydrogen bonds : angle 3.73857 ( 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 176 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 638 MET cc_start: 0.8467 (ttt) cc_final: 0.8109 (mmt) REVERT: A 686 MET cc_start: 0.7927 (tpp) cc_final: 0.7552 (tpp) REVERT: B 298 LYS cc_start: 0.9495 (mttt) cc_final: 0.9150 (mttp) REVERT: B 402 MET cc_start: 0.2977 (mmp) cc_final: 0.2613 (mmt) REVERT: B 452 TRP cc_start: 0.7239 (t60) cc_final: 0.6974 (t60) REVERT: C 479 LEU cc_start: 0.9179 (tp) cc_final: 0.8927 (pp) REVERT: C 505 MET cc_start: 0.7226 (tmm) cc_final: 0.6735 (tmm) REVERT: C 638 MET cc_start: 0.8830 (ttt) cc_final: 0.8399 (mmt) REVERT: C 686 MET cc_start: 0.7954 (tpp) cc_final: 0.7568 (tpp) REVERT: D 97 LEU cc_start: 0.9458 (tp) cc_final: 0.9248 (pp) REVERT: D 505 MET cc_start: 0.5491 (tpp) cc_final: 0.5018 (tpp) outliers start: 21 outliers final: 16 residues processed: 170 average time/residue: 0.0955 time to fit residues: 27.8487 Evaluate side-chains 162 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 343 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 6.9990 chunk 168 optimal weight: 0.2980 chunk 180 optimal weight: 0.0270 chunk 55 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.120405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088837 restraints weight = 57284.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091377 restraints weight = 29770.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093034 restraints weight = 19722.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094054 restraints weight = 15080.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094612 restraints weight = 12722.085| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3905 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= 0.101 Angle : 0.588 15.656 23698 Z= 0.274 Chirality : 0.040 0.290 2796 Planarity : 0.003 0.047 3044 Dihedral : 5.590 87.899 2884 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.45 % Allowed : 14.95 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.18), residues: 2358 helix: 2.40 (0.14), residues: 1488 sheet: 0.63 (0.56), residues: 80 loop : 0.14 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.023 0.001 TYR B 542 PHE 0.013 0.001 PHE B 599 TRP 0.013 0.001 TRP A 655 HIS 0.002 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00218 (17246) covalent geometry : angle 0.58840 (23698) hydrogen bonds : bond 0.02894 ( 1111) hydrogen bonds : angle 3.73037 ( 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 183 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 638 MET cc_start: 0.8591 (ttt) cc_final: 0.8167 (mmt) REVERT: A 686 MET cc_start: 0.7849 (tpp) cc_final: 0.7460 (tpp) REVERT: B 298 LYS cc_start: 0.9508 (mttt) cc_final: 0.9221 (mttp) REVERT: B 402 MET cc_start: 0.2841 (mmp) cc_final: 0.2512 (mmt) REVERT: B 452 TRP cc_start: 0.7122 (t60) cc_final: 0.6866 (t60) REVERT: B 686 MET cc_start: 0.9283 (mmm) cc_final: 0.9002 (mmt) REVERT: C 226 TYR cc_start: 0.8868 (t80) cc_final: 0.8610 (t80) REVERT: C 479 LEU cc_start: 0.9185 (tp) cc_final: 0.8950 (pp) REVERT: C 505 MET cc_start: 0.6916 (tmm) cc_final: 0.6483 (tmm) REVERT: C 638 MET cc_start: 0.8827 (ttt) cc_final: 0.8407 (mmt) REVERT: C 686 MET cc_start: 0.7968 (tpp) cc_final: 0.7562 (tpp) REVERT: D 97 LEU cc_start: 0.9496 (tp) cc_final: 0.9273 (pp) REVERT: D 505 MET cc_start: 0.5569 (tpp) cc_final: 0.5132 (tpp) REVERT: D 605 MET cc_start: 0.2091 (mmt) cc_final: 0.1695 (mtp) REVERT: D 686 MET cc_start: 0.9267 (mmm) cc_final: 0.8978 (mmt) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 0.0960 time to fit residues: 29.0763 Evaluate side-chains 170 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 343 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 LEU 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: 30.0000 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087713 restraints weight = 58395.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090134 restraints weight = 31141.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091686 restraints weight = 20859.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092759 restraints weight = 16233.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093331 restraints weight = 13830.753| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17246 Z= 0.155 Angle : 0.618 15.479 23698 Z= 0.293 Chirality : 0.040 0.278 2796 Planarity : 0.004 0.047 3044 Dihedral : 5.601 89.035 2884 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.45 % Allowed : 15.38 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.13), residues: 1488 sheet: 0.45 (0.57), residues: 80 loop : 0.13 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 682 TYR 0.018 0.001 TYR D 627 PHE 0.016 0.001 PHE C 405 TRP 0.021 0.001 TRP C 507 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00345 (17246) covalent geometry : angle 0.61751 (23698) hydrogen bonds : bond 0.03145 ( 1111) hydrogen bonds : angle 3.84959 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.64 seconds wall clock time: 49 minutes 18.73 seconds (2958.73 seconds total)