Starting phenix.real_space_refine on Tue Dec 31 13:53:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk7_34848/12_2024/8hk7_34848_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 10428 2.51 5 N 2460 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' CA': 1, 'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.89, per 1000 atoms: 0.63 Number of scatterers: 15765 At special positions: 0 Unit cell: (108.7, 108.7, 102.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 80 16.00 O 2796 8.00 N 2460 7.00 C 10428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 328 " " NAG A1002 " - " ASN A 362 " " NAG A1003 " - " ASN A 375 " " NAG B1001 " - " ASN B 328 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 375 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 375 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 12 sheets defined 58.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.706A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 335 through 339 removed outlier: 4.572A pdb=" N ASP A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 4.011A pdb=" N TRP A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 495 removed outlier: 3.612A pdb=" N PHE A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 removed outlier: 4.458A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.989A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 5.982A pdb=" N THR A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 removed outlier: 3.528A pdb=" N ALA A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.784A pdb=" N SER A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.598A pdb=" N ILE A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.632A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 687 removed outlier: 3.606A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.704A pdb=" N THR B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.558A pdb=" N ASP B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 4.014A pdb=" N TRP B 366 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 367' Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.510A pdb=" N THR B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 494 removed outlier: 3.610A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 removed outlier: 3.508A pdb=" N VAL B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.039A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.721A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 601 Processing helix chain 'B' and resid 601 through 619 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.781A pdb=" N SER B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 628 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.594A pdb=" N ILE B 633 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.658A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 687 removed outlier: 3.613A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.706A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 335 through 339 removed outlier: 4.554A pdb=" N ASP C 339 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 4.012A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.602A pdb=" N PHE C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 530 removed outlier: 4.275A pdb=" N VAL C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 541 Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.957A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 578' Processing helix chain 'C' and resid 579 through 584 removed outlier: 6.004A pdb=" N THR C 582 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER C 584 " --> pdb=" O ARG C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 591 removed outlier: 3.823A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 601 through 619 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.806A pdb=" N SER C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 628 " --> pdb=" O ASP C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.596A pdb=" N ILE C 633 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.660A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 687 removed outlier: 3.595A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.707A pdb=" N THR D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 335 through 339 removed outlier: 4.604A pdb=" N ASP D 339 " --> pdb=" O ASP D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 removed outlier: 4.010A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 494 removed outlier: 3.597A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 528 removed outlier: 4.440A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.912A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 592 Processing helix chain 'D' and resid 601 through 619 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.779A pdb=" N SER D 627 " --> pdb=" O ASP D 624 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 628 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.593A pdb=" N ILE D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.664A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 687 removed outlier: 3.609A pdb=" N ILE D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.685A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.685A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.688A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.688A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.684A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.684A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.658A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.658A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 861 hydrogen bonds defined for protein. 2463 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: 5.21 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2408 1.30 - 1.43: 4742 1.43 - 1.56: 8915 1.56 - 1.68: 7 1.68 - 1.81: 124 Bond restraints: 16196 Sorted by residual: bond pdb=" C1 AQV A1005 " pdb=" C2 AQV A1005 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C1 AQV D1004 " pdb=" C2 AQV D1004 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C1 AQV C1004 " pdb=" C2 AQV C1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C1 AQV B1004 " pdb=" C2 AQV B1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C5 AQV A1005 " pdb=" C6 AQV A1005 " ideal model delta sigma weight residual 1.381 1.543 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 16191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 21400 2.02 - 4.04: 497 4.04 - 6.06: 72 6.06 - 8.08: 22 8.08 - 10.10: 9 Bond angle restraints: 22000 Sorted by residual: angle pdb=" N SER B 587 " pdb=" CA SER B 587 " pdb=" C SER B 587 " ideal model delta sigma weight residual 110.97 103.01 7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N SER A 587 " pdb=" CA SER A 587 " pdb=" C SER A 587 " ideal model delta sigma weight residual 110.80 102.00 8.80 2.13e+00 2.20e-01 1.71e+01 angle pdb=" N THR B 589 " pdb=" CA THR B 589 " pdb=" C THR B 589 " ideal model delta sigma weight residual 111.28 115.76 -4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" C PHE B 310 " pdb=" N TYR B 311 " pdb=" CA TYR B 311 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C PHE D 310 " pdb=" N TYR D 311 " pdb=" CA TYR D 311 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 21995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 9299 35.50 - 71.00: 191 71.00 - 106.50: 46 106.50 - 142.00: 4 142.00 - 177.49: 8 Dihedral angle restraints: 9548 sinusoidal: 4000 harmonic: 5548 Sorted by residual: dihedral pdb=" CA CYS C 331 " pdb=" C CYS C 331 " pdb=" N SER C 332 " pdb=" CA SER C 332 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA CYS D 331 " pdb=" C CYS D 331 " pdb=" N SER D 332 " pdb=" CA SER D 332 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA CYS B 331 " pdb=" C CYS B 331 " pdb=" N SER B 332 " pdb=" CA SER B 332 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1643 0.037 - 0.074: 574 0.074 - 0.110: 189 0.110 - 0.147: 52 0.147 - 0.184: 10 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA SER A 587 " pdb=" N SER A 587 " pdb=" C SER A 587 " pdb=" CB SER A 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA SER B 587 " pdb=" N SER B 587 " pdb=" C SER B 587 " pdb=" CB SER B 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA ARG B 592 " pdb=" N ARG B 592 " pdb=" C ARG B 592 " pdb=" CB ARG B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2465 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 585 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C GLN A 585 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN A 585 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 585 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLN C 585 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN C 585 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU C 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 585 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLN B 585 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 585 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 586 " 0.014 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 12 2.24 - 2.91: 6670 2.91 - 3.57: 22302 3.57 - 4.24: 34906 4.24 - 4.90: 62124 Nonbonded interactions: 126014 Sorted by model distance: nonbonded pdb=" CE1 TYR A 684 " pdb=" OH TYR D 684 " model vdw 1.579 3.340 nonbonded pdb=" O GLN D 585 " pdb=" CG2 THR D 589 " model vdw 1.990 3.460 nonbonded pdb=" OH TYR D 386 " pdb=" OE1 GLU D 444 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" OE1 GLU A 444 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" OE1 GLU B 444 " model vdw 2.203 3.040 ... (remaining 126009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'B' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'C' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'D' and (resid 215 through 688 or resid 1001 through 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.380 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.070 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:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4027 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 : 0.009 0.167 16196 Z= 0.553 Angle : 0.748 10.097 22000 Z= 0.403 Chirality : 0.044 0.184 2468 Planarity : 0.004 0.037 2708 Dihedral : 16.919 177.494 5952 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 0.53 % Allowed : 0.88 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1856 helix: 0.45 (0.17), residues: 924 sheet: -1.09 (0.37), residues: 176 loop : -1.72 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS B 501 PHE 0.028 0.001 PHE C 483 TYR 0.023 0.001 TYR D 249 ARG 0.005 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 458 time to evaluate : 1.594 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 583 MET cc_start: 0.4029 (ppp) cc_final: 0.3825 (ttt) REVERT: B 478 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (pt) REVERT: B 482 PHE cc_start: 0.8466 (m-10) cc_final: 0.7895 (t80) REVERT: B 649 ILE cc_start: 0.8323 (mt) cc_final: 0.8063 (OUTLIER) REVERT: D 256 LEU cc_start: 0.2769 (tp) cc_final: 0.2512 (mt) REVERT: D 345 TYR cc_start: 0.4546 (m-80) cc_final: 0.0840 (m-80) outliers start: 9 outliers final: 3 residues processed: 463 average time/residue: 1.0032 time to fit residues: 527.7103 Evaluate side-chains 264 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain D residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.0050 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 overall best weight: 1.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 458 GLN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 585 GLN B 313 ASN B 412 ASN B 531 ASN B 547 ASN B 636 GLN C 313 ASN C 323 GLN C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 636 GLN C 674 ASN D 323 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 578 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16196 Z= 0.268 Angle : 0.828 11.691 22000 Z= 0.413 Chirality : 0.046 0.198 2468 Planarity : 0.005 0.058 2708 Dihedral : 17.920 169.282 2402 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 4.42 % Allowed : 13.38 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1856 helix: 0.48 (0.16), residues: 984 sheet: -0.91 (0.40), residues: 192 loop : -1.60 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 293 HIS 0.004 0.001 HIS C 379 PHE 0.048 0.003 PHE C 664 TYR 0.022 0.002 TYR A 249 ARG 0.009 0.001 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4984 (pp) REVERT: B 295 MET cc_start: 0.5922 (mmm) cc_final: 0.5711 (mmp) REVERT: B 482 PHE cc_start: 0.8592 (m-10) cc_final: 0.8103 (t80) REVERT: B 595 LYS cc_start: 0.5545 (OUTLIER) cc_final: 0.4922 (tptm) REVERT: C 307 SER cc_start: 0.7773 (OUTLIER) cc_final: 0.7544 (t) REVERT: C 310 PHE cc_start: 0.7470 (m-10) cc_final: 0.6354 (m-80) REVERT: D 245 ASN cc_start: 0.7174 (t0) cc_final: 0.6882 (p0) REVERT: D 315 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2544 (tt) REVERT: D 484 ILE cc_start: 0.3428 (OUTLIER) cc_final: 0.3216 (pt) outliers start: 75 outliers final: 19 residues processed: 344 average time/residue: 0.8433 time to fit residues: 337.0059 Evaluate side-chains 248 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 0.0270 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 269 ASN A 335 GLN A 456 GLN A 508 ASN A 585 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 559 ASN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN D 245 ASN D 323 GLN D 379 HIS D 456 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 1.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16196 Z= 0.335 Angle : 0.953 13.871 22000 Z= 0.474 Chirality : 0.049 0.333 2468 Planarity : 0.006 0.071 2708 Dihedral : 16.790 173.595 2400 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.03 % Rotamer: Outliers : 5.42 % Allowed : 18.46 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1856 helix: 0.41 (0.16), residues: 972 sheet: -0.58 (0.42), residues: 156 loop : -2.27 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 293 HIS 0.003 0.001 HIS D 498 PHE 0.035 0.003 PHE D 457 TYR 0.029 0.002 TYR B 249 ARG 0.010 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 309 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7934 (t0) cc_final: 0.7733 (t0) REVERT: A 456 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7808 (pp30) REVERT: A 507 TRP cc_start: 0.5932 (m100) cc_final: 0.4675 (p90) REVERT: A 585 GLN cc_start: -0.2469 (OUTLIER) cc_final: -0.3039 (pt0) REVERT: B 482 PHE cc_start: 0.8594 (m-10) cc_final: 0.8322 (t80) REVERT: B 595 LYS cc_start: 0.5444 (OUTLIER) cc_final: 0.5034 (tmtt) REVERT: C 242 MET cc_start: 0.7333 (tpp) cc_final: 0.7105 (tpp) REVERT: C 278 ASP cc_start: 0.7725 (m-30) cc_final: 0.7517 (m-30) REVERT: D 255 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8254 (pp30) REVERT: D 442 LEU cc_start: 0.7986 (tp) cc_final: 0.7751 (tp) outliers start: 92 outliers final: 23 residues processed: 375 average time/residue: 0.7928 time to fit residues: 348.2578 Evaluate side-chains 229 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN D 432 ASN D 434 ASN D 557 GLN D 559 ASN D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 1.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16196 Z= 0.190 Angle : 0.784 11.990 22000 Z= 0.374 Chirality : 0.044 0.238 2468 Planarity : 0.004 0.047 2708 Dihedral : 16.717 176.072 2400 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.54 % Allowed : 22.94 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1856 helix: 0.83 (0.16), residues: 972 sheet: -0.76 (0.42), residues: 164 loop : -2.10 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 414 HIS 0.002 0.000 HIS A 379 PHE 0.023 0.002 PHE B 426 TYR 0.020 0.001 TYR A 227 ARG 0.005 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 245 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 482 PHE cc_start: 0.8541 (m-10) cc_final: 0.8289 (t80) REVERT: B 595 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5335 (tmtt) REVERT: C 236 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7943 (tp) REVERT: D 471 PHE cc_start: 0.5493 (m-80) cc_final: 0.5020 (t80) outliers start: 77 outliers final: 23 residues processed: 301 average time/residue: 0.7873 time to fit residues: 278.3434 Evaluate side-chains 229 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 313 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN D 432 ASN D 531 ASN D 557 GLN D 578 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 1.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16196 Z= 0.260 Angle : 0.840 11.254 22000 Z= 0.408 Chirality : 0.047 0.288 2468 Planarity : 0.004 0.037 2708 Dihedral : 16.981 175.737 2400 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.42 % Allowed : 23.29 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1856 helix: 0.86 (0.16), residues: 936 sheet: -0.88 (0.41), residues: 164 loop : -2.19 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 414 HIS 0.003 0.001 HIS D 550 PHE 0.035 0.002 PHE D 483 TYR 0.018 0.002 TYR A 348 ARG 0.006 0.001 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 243 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 CYS cc_start: 0.3740 (OUTLIER) cc_final: 0.2204 (m) REVERT: B 295 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.4912 (mtt) REVERT: B 333 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7644 (tp) REVERT: B 341 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7604 (mp) REVERT: B 595 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5817 (tmtt) REVERT: C 236 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8271 (tp) REVERT: C 242 MET cc_start: 0.7589 (tpp) cc_final: 0.7326 (tpp) REVERT: C 278 ASP cc_start: 0.7566 (m-30) cc_final: 0.6974 (m-30) REVERT: D 253 MET cc_start: 0.8067 (tpp) cc_final: 0.7685 (mmm) REVERT: D 293 TRP cc_start: 0.8092 (m100) cc_final: 0.7888 (m-10) REVERT: D 471 PHE cc_start: 0.5717 (m-80) cc_final: 0.5008 (t80) REVERT: D 545 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: D 609 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8601 (mm) REVERT: D 675 MET cc_start: 0.4335 (mmp) cc_final: 0.4076 (mmp) outliers start: 92 outliers final: 17 residues processed: 310 average time/residue: 0.8294 time to fit residues: 300.8030 Evaluate side-chains 212 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 147 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 412 ASN D 557 GLN D 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 1.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16196 Z= 0.192 Angle : 0.790 14.073 22000 Z= 0.371 Chirality : 0.044 0.243 2468 Planarity : 0.004 0.037 2708 Dihedral : 16.708 177.044 2400 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.36 % Allowed : 28.66 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1856 helix: 0.98 (0.16), residues: 940 sheet: -0.82 (0.42), residues: 164 loop : -2.17 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 414 HIS 0.001 0.000 HIS C 501 PHE 0.024 0.002 PHE C 605 TYR 0.020 0.001 TYR B 239 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ILE cc_start: 0.8649 (pt) cc_final: 0.8221 (mm) REVERT: A 593 CYS cc_start: 0.3764 (OUTLIER) cc_final: 0.2175 (m) REVERT: B 295 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5292 (mtt) REVERT: B 341 ILE cc_start: 0.7902 (pp) cc_final: 0.7463 (mp) REVERT: B 595 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5749 (tmtt) REVERT: B 611 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8229 (t80) REVERT: C 236 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8323 (tp) REVERT: C 242 MET cc_start: 0.7691 (tpp) cc_final: 0.7457 (tpp) REVERT: D 471 PHE cc_start: 0.5524 (m-80) cc_final: 0.5220 (t80) outliers start: 57 outliers final: 23 residues processed: 259 average time/residue: 0.7765 time to fit residues: 237.7645 Evaluate side-chains 217 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 ASN D 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 1.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16196 Z= 0.244 Angle : 0.832 10.139 22000 Z= 0.398 Chirality : 0.046 0.211 2468 Planarity : 0.004 0.041 2708 Dihedral : 16.883 177.124 2400 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.48 % Allowed : 29.66 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1856 helix: 0.81 (0.16), residues: 964 sheet: -0.94 (0.41), residues: 164 loop : -2.13 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 507 HIS 0.003 0.001 HIS D 379 PHE 0.028 0.002 PHE D 423 TYR 0.027 0.002 TYR C 502 ARG 0.006 0.001 ARG C 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 CYS cc_start: 0.4004 (OUTLIER) cc_final: 0.2327 (m) REVERT: B 341 ILE cc_start: 0.7873 (pp) cc_final: 0.7509 (mp) REVERT: B 595 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5604 (tmtt) REVERT: B 611 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8456 (t80) REVERT: C 236 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 278 ASP cc_start: 0.7501 (m-30) cc_final: 0.7204 (m-30) REVERT: C 477 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 517 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7953 (mp) REVERT: C 583 MET cc_start: -0.0112 (mmp) cc_final: -0.0537 (mmm) REVERT: D 293 TRP cc_start: 0.8063 (m100) cc_final: 0.7858 (m-10) REVERT: D 477 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5500 (pp20) REVERT: D 506 PHE cc_start: 0.6233 (t80) cc_final: 0.5615 (p90) REVERT: D 670 PHE cc_start: 0.7522 (t80) cc_final: 0.7220 (t80) outliers start: 59 outliers final: 24 residues processed: 270 average time/residue: 0.8159 time to fit residues: 256.7190 Evaluate side-chains 218 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 508 ASN D 578 ASN D 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 1.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16196 Z= 0.212 Angle : 0.829 11.053 22000 Z= 0.394 Chirality : 0.045 0.278 2468 Planarity : 0.004 0.043 2708 Dihedral : 16.827 177.752 2400 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.12 % Allowed : 32.55 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1856 helix: 0.78 (0.16), residues: 964 sheet: -0.81 (0.42), residues: 164 loop : -2.22 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 366 HIS 0.001 0.000 HIS A 498 PHE 0.043 0.002 PHE B 485 TYR 0.025 0.001 TYR A 527 ARG 0.007 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 CYS cc_start: 0.4124 (OUTLIER) cc_final: 0.2404 (m) REVERT: B 341 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7384 (mp) REVERT: B 595 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5625 (tmtt) REVERT: B 611 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8369 (t80) REVERT: C 236 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 259 ASP cc_start: 0.8016 (m-30) cc_final: 0.7806 (m-30) REVERT: C 278 ASP cc_start: 0.7602 (m-30) cc_final: 0.7350 (m-30) REVERT: C 477 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 502 TYR cc_start: 0.5488 (t80) cc_final: 0.5037 (t80) REVERT: D 506 PHE cc_start: 0.6420 (t80) cc_final: 0.5792 (p90) REVERT: D 522 ILE cc_start: 0.8488 (tp) cc_final: 0.8131 (tt) REVERT: D 670 PHE cc_start: 0.7565 (t80) cc_final: 0.7356 (t80) outliers start: 36 outliers final: 16 residues processed: 242 average time/residue: 0.7867 time to fit residues: 223.4882 Evaluate side-chains 209 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 149 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN D 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 1.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16196 Z= 0.226 Angle : 0.848 11.397 22000 Z= 0.405 Chirality : 0.045 0.241 2468 Planarity : 0.004 0.043 2708 Dihedral : 16.851 178.364 2400 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.83 % Allowed : 33.31 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1856 helix: 0.94 (0.16), residues: 940 sheet: -0.79 (0.42), residues: 176 loop : -2.30 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 455 HIS 0.002 0.000 HIS D 498 PHE 0.043 0.002 PHE C 600 TYR 0.031 0.001 TYR B 348 ARG 0.008 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.5712 (tmm) cc_final: 0.4707 (ttt) REVERT: A 593 CYS cc_start: 0.4022 (OUTLIER) cc_final: 0.2309 (m) REVERT: B 341 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 595 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5610 (tmtt) REVERT: B 611 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 675 MET cc_start: 0.6101 (mmp) cc_final: 0.5893 (tpp) REVERT: C 236 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8498 (tt) REVERT: C 245 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.6995 (t0) REVERT: C 259 ASP cc_start: 0.8075 (m-30) cc_final: 0.7856 (m-30) REVERT: C 278 ASP cc_start: 0.7616 (m-30) cc_final: 0.7371 (m-30) REVERT: C 477 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 502 TYR cc_start: 0.5400 (t80) cc_final: 0.4789 (t80) REVERT: C 531 ASN cc_start: 0.7341 (t0) cc_final: 0.6596 (m110) REVERT: C 583 MET cc_start: 0.0182 (mmp) cc_final: -0.0260 (mmm) REVERT: D 228 LEU cc_start: 0.8790 (tt) cc_final: 0.8565 (tt) REVERT: D 369 THR cc_start: 0.7597 (m) cc_final: 0.7378 (p) REVERT: D 506 PHE cc_start: 0.6512 (t80) cc_final: 0.6210 (p90) REVERT: D 522 ILE cc_start: 0.8680 (tp) cc_final: 0.8291 (tt) REVERT: D 673 LEU cc_start: 0.8642 (mp) cc_final: 0.8378 (mp) outliers start: 31 outliers final: 17 residues processed: 235 average time/residue: 0.7828 time to fit residues: 217.5640 Evaluate side-chains 212 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN C 578 ASN D 245 ASN D 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 1.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16196 Z= 0.299 Angle : 0.903 13.829 22000 Z= 0.435 Chirality : 0.047 0.234 2468 Planarity : 0.005 0.044 2708 Dihedral : 17.105 178.312 2400 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.18 % Allowed : 33.43 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1856 helix: 0.57 (0.16), residues: 980 sheet: -0.84 (0.42), residues: 164 loop : -2.46 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 366 HIS 0.002 0.001 HIS A 498 PHE 0.029 0.002 PHE B 485 TYR 0.024 0.002 TYR D 611 ARG 0.008 0.001 ARG D 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.6175 (tmm) cc_final: 0.5528 (ttt) REVERT: A 593 CYS cc_start: 0.4272 (OUTLIER) cc_final: 0.2591 (m) REVERT: B 237 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 341 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7391 (mp) REVERT: B 595 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5370 (tmtt) REVERT: B 611 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8367 (t80) REVERT: C 236 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (tt) REVERT: C 245 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7146 (t0) REVERT: C 531 ASN cc_start: 0.7790 (t0) cc_final: 0.6972 (m110) REVERT: C 583 MET cc_start: 0.0527 (OUTLIER) cc_final: 0.0150 (mmm) REVERT: D 669 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5768 (t80) REVERT: D 673 LEU cc_start: 0.8743 (mp) cc_final: 0.8517 (mp) outliers start: 37 outliers final: 18 residues processed: 217 average time/residue: 0.7472 time to fit residues: 192.2749 Evaluate side-chains 193 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 669 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 146 optimal weight: 0.0030 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN D 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.118270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093927 restraints weight = 33087.163| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.55 r_work: 0.3348 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 1.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16196 Z= 0.237 Angle : 0.851 11.722 22000 Z= 0.408 Chirality : 0.045 0.236 2468 Planarity : 0.005 0.120 2708 Dihedral : 17.040 178.175 2400 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.00 % Allowed : 34.20 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1856 helix: 0.83 (0.16), residues: 964 sheet: -0.79 (0.43), residues: 164 loop : -2.50 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 455 HIS 0.002 0.000 HIS C 498 PHE 0.034 0.002 PHE D 506 TYR 0.031 0.002 TYR B 348 ARG 0.016 0.001 ARG D 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4927.81 seconds wall clock time: 90 minutes 1.32 seconds (5401.32 seconds total)