Starting phenix.real_space_refine on Fri Jul 3 19:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_34848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_34848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_34848_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_34848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk7_34848/07_2026/8hk7_34848.map" } resolution = 3.0 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 69 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 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: 3.29, per 1000 atoms: 0.21 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: 1.48 Conformation dependent library (CDL) restraints added in 821.5 milliseconds 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: 0.67 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: 3.21 Time building geometry restraints manager: 1.99 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 1003) selection = (chain 'B' and resid 215 through 1003) selection = (chain 'C' and resid 215 through 1003) selection = (chain 'D' and resid 215 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: 0.900 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.440 Find NCS groups from input model: 0.390 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3857 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 16212 Z= 0.456 Angle : 0.826 18.235 22044 Z= 0.421 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 : 11.78 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 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: -0.87 (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 ARG 0.005 0.000 ARG B 306 TYR 0.023 0.001 TYR D 249 PHE 0.028 0.001 PHE C 483 TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.46 (16196) covalent geometry : angle 0.74807 / 0.40 (22000) SS BOND : bond 0.00321 / 0.20 ( 4) SS BOND : angle 4.02232 / 2.03 ( 8) hydrogen bonds : bond 0.16807 / 10.63 ( 805) hydrogen bonds : angle 5.76442 / 3.95 ( 2463) link_NAG-ASN : bond 0.01581 / 1.06 ( 12) link_NAG-ASN : angle 8.50606 / 6.19 ( 36) *********************** 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 : 0.624 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: 0.4348 time to fit residues: 229.1968 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 : 0.566 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 379 HIS A 458 GLN A 508 ASN A 578 ASN A 585 GLN B 313 ASN B 456 GLN B 531 ASN B 547 ASN B 636 GLN C 313 ASN C 323 GLN C 412 ASN C 613 GLN C 636 GLN C 674 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 HIS D 458 GLN D 501 HIS ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.144255 restraints weight = 33793.496| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 4.13 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.8143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16212 Z= 0.278 Angle : 0.990 17.569 22044 Z= 0.492 Chirality : 0.051 0.234 2468 Planarity : 0.006 0.073 2708 Dihedral : 17.954 168.442 2402 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.86 % Rotamer: Outliers : 4.95 % Allowed : 13.86 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1856 helix: 0.26 (0.16), residues: 940 sheet: -0.72 (0.42), residues: 164 loop : -2.02 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 222 TYR 0.028 0.003 TYR B 684 PHE 0.051 0.003 PHE C 664 TRP 0.037 0.003 TRP A 366 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 (16196) covalent geometry : angle 0.94217 / 0.48 (22000) SS BOND : bond 0.03158 / 1.58 ( 4) SS BOND : angle 4.70545 / 2.37 ( 8) hydrogen bonds : bond 0.06032 / 3.81 ( 805) hydrogen bonds : angle 4.84681 / 3.38 ( 2463) link_NAG-ASN : bond 0.01661 / 1.13 ( 12) link_NAG-ASN : angle 7.29134 / 5.34 ( 36) *********************** 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 420 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 336 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5612 (tpp) REVERT: A 280 TRP cc_start: 0.6606 (OUTLIER) cc_final: 0.5723 (m-10) REVERT: A 340 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: A 379 HIS cc_start: 0.5405 (OUTLIER) cc_final: 0.4648 (p-80) REVERT: A 507 TRP cc_start: 0.5700 (m100) cc_final: 0.3935 (p90) REVERT: A 583 MET cc_start: 0.5485 (ppp) cc_final: 0.4942 (ttt) REVERT: B 308 PHE cc_start: 0.7722 (m-10) cc_final: 0.7513 (m-10) REVERT: B 330 SER cc_start: 0.8135 (t) cc_final: 0.7858 (p) REVERT: B 348 TYR cc_start: 0.8782 (t80) cc_final: 0.7981 (t80) REVERT: B 406 VAL cc_start: 0.8854 (t) cc_final: 0.8594 (m) REVERT: B 482 PHE cc_start: 0.8782 (m-10) cc_final: 0.8192 (t80) REVERT: B 595 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4769 (tttt) REVERT: B 668 MET cc_start: 0.4534 (OUTLIER) cc_final: 0.4322 (mmp) REVERT: C 236 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7647 (tp) REVERT: C 307 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.7914 (t) REVERT: C 414 TRP cc_start: 0.8764 (OUTLIER) cc_final: 0.8014 (t60) REVERT: C 442 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8964 (tp) REVERT: C 448 THR cc_start: 0.7771 (p) cc_final: 0.7158 (p) REVERT: D 295 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4367 (tmm) REVERT: D 484 ILE cc_start: 0.4806 (OUTLIER) cc_final: 0.4520 (pt) REVERT: D 592 ARG cc_start: 0.7677 (mmt180) cc_final: 0.7075 (mmm160) outliers start: 84 outliers final: 21 residues processed: 388 average time/residue: 0.3875 time to fit residues: 174.2908 Evaluate side-chains 258 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 621 THR 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 506 PHE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 220 VAL 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 374 LEU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 295 MET 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 485 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 8 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 585 GLN B 412 ASN B 458 GLN C 547 ASN C 559 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.163837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.139215 restraints weight = 32894.361| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.00 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.9416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16212 Z= 0.150 Angle : 0.807 17.247 22044 Z= 0.377 Chirality : 0.043 0.170 2468 Planarity : 0.004 0.054 2708 Dihedral : 16.994 176.991 2400 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.19 % Allowed : 19.87 % Favored : 75.94 % 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: -0.54 (0.20), residues: 1856 helix: 0.87 (0.17), residues: 968 sheet: -0.67 (0.42), residues: 164 loop : -2.01 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 592 TYR 0.026 0.001 TYR C 348 PHE 0.023 0.002 PHE B 669 TRP 0.028 0.002 TRP D 414 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (16196) covalent geometry : angle 0.75238 / 0.36 (22000) SS BOND : bond 0.00496 / 0.25 ( 4) SS BOND : angle 2.56647 / 1.37 ( 8) hydrogen bonds : bond 0.04441 / 2.80 ( 805) hydrogen bonds : angle 4.05861 / 2.78 ( 2463) link_NAG-ASN : bond 0.01466 / 0.99 ( 12) link_NAG-ASN : angle 7.13756 / 5.28 ( 36) *********************** 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 333 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5699 (tpp) REVERT: A 252 MET cc_start: 0.6967 (tpt) cc_final: 0.6638 (tpt) REVERT: A 324 LEU cc_start: 0.8817 (tp) cc_final: 0.8287 (tp) REVERT: A 335 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7355 (mt0) REVERT: A 440 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7152 (tpp80) REVERT: A 507 TRP cc_start: 0.5860 (m100) cc_final: 0.4255 (p90) REVERT: A 583 MET cc_start: 0.5896 (ppp) cc_final: 0.5451 (ttt) REVERT: A 585 GLN cc_start: -0.1405 (OUTLIER) cc_final: -0.1929 (pt0) REVERT: A 617 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7763 (mm) REVERT: B 242 MET cc_start: 0.7085 (tpt) cc_final: 0.6830 (tpp) REVERT: B 273 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8098 (mp) REVERT: B 312 GLU cc_start: 0.7436 (pt0) cc_final: 0.7056 (pm20) REVERT: B 433 ILE cc_start: 0.8089 (pp) cc_final: 0.7879 (pp) REVERT: B 482 PHE cc_start: 0.8739 (m-10) cc_final: 0.8173 (t80) REVERT: B 487 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7217 (t80) REVERT: B 595 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4816 (tmtt) REVERT: B 611 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7453 (t80) REVERT: C 278 ASP cc_start: 0.7522 (m-30) cc_final: 0.7132 (m-30) REVERT: C 312 GLU cc_start: 0.7800 (pt0) cc_final: 0.7591 (pt0) REVERT: C 522 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7982 (tt) REVERT: D 295 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.4736 (tmm) REVERT: D 485 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6235 (t80) REVERT: D 593 CYS cc_start: 0.2518 (p) cc_final: 0.2158 (m) outliers start: 71 outliers final: 16 residues processed: 312 average time/residue: 0.3490 time to fit residues: 128.0626 Evaluate side-chains 233 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 559 ASN C 323 GLN C 555 GLN C 559 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.151139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.125880 restraints weight = 32105.831| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.87 r_work: 0.3768 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 1.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16212 Z= 0.162 Angle : 0.825 15.568 22044 Z= 0.384 Chirality : 0.045 0.243 2468 Planarity : 0.005 0.090 2708 Dihedral : 16.548 175.930 2400 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.78 % Allowed : 21.52 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1856 helix: 1.08 (0.17), residues: 948 sheet: -0.75 (0.42), residues: 164 loop : -1.92 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 338 TYR 0.021 0.002 TYR A 429 PHE 0.023 0.002 PHE B 426 TRP 0.026 0.002 TRP D 280 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16196) covalent geometry : angle 0.78287 / 0.37 (22000) SS BOND : bond 0.00457 / 0.31 ( 4) SS BOND : angle 2.07874 / 1.06 ( 8) hydrogen bonds : bond 0.04280 / 2.71 ( 805) hydrogen bonds : angle 3.96301 / 2.70 ( 2463) link_NAG-ASN : bond 0.01534 / 0.99 ( 12) link_NAG-ASN : angle 6.40634 / 4.86 ( 36) *********************** 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 352 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 271 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3510 (OUTLIER) cc_final: 0.3299 (tm) REVERT: A 242 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6004 (tpp) REVERT: A 252 MET cc_start: 0.7711 (tpt) cc_final: 0.7505 (tpt) REVERT: A 335 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7745 (mt0) REVERT: A 340 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: A 583 MET cc_start: 0.5402 (ppp) cc_final: 0.5033 (ttm) REVERT: B 229 LEU cc_start: 0.8858 (mm) cc_final: 0.8605 (mp) REVERT: B 273 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 312 GLU cc_start: 0.7829 (pt0) cc_final: 0.7617 (pt0) REVERT: B 353 GLU cc_start: 0.9080 (tt0) cc_final: 0.8814 (tp30) REVERT: B 406 VAL cc_start: 0.8737 (t) cc_final: 0.8533 (m) REVERT: B 502 TYR cc_start: 0.6927 (t80) cc_final: 0.6475 (t80) REVERT: B 503 PHE cc_start: 0.5318 (p90) cc_final: 0.4996 (m-10) REVERT: B 595 LYS cc_start: 0.5723 (OUTLIER) cc_final: 0.5261 (tmtt) REVERT: B 611 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 669 PHE cc_start: 0.6110 (p90) cc_final: 0.5710 (m-10) REVERT: B 675 MET cc_start: 0.5547 (mmp) cc_final: 0.5323 (mmp) REVERT: C 236 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7523 (tp) REVERT: C 278 ASP cc_start: 0.8221 (m-30) cc_final: 0.7763 (m-30) REVERT: C 517 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7195 (mp) REVERT: C 522 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8073 (tt) REVERT: C 592 ARG cc_start: 0.6955 (tmm160) cc_final: 0.6652 (tmm160) REVERT: C 637 PHE cc_start: 0.8740 (m-80) cc_final: 0.8163 (m-80) REVERT: D 255 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8501 (pp30) REVERT: D 276 MET cc_start: 0.7432 (ppp) cc_final: 0.7223 (ptp) REVERT: D 291 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7773 (tp) REVERT: D 295 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5370 (tmm) REVERT: D 324 LEU cc_start: 0.6654 (mt) cc_final: 0.6365 (mm) REVERT: D 344 CYS cc_start: 0.4163 (OUTLIER) cc_final: 0.3604 (t) REVERT: D 433 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7742 (pp) REVERT: D 471 PHE cc_start: 0.6719 (m-80) cc_final: 0.5411 (t80) REVERT: D 485 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6613 (t80) REVERT: D 590 MET cc_start: 0.6904 (tpp) cc_final: 0.6586 (tpp) REVERT: D 593 CYS cc_start: 0.3251 (p) cc_final: 0.2828 (m) REVERT: D 611 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7491 (t80) REVERT: D 633 ILE cc_start: 0.8024 (mm) cc_final: 0.7723 (mm) REVERT: D 637 PHE cc_start: 0.8668 (m-80) cc_final: 0.8156 (m-80) outliers start: 81 outliers final: 25 residues processed: 328 average time/residue: 0.3531 time to fit residues: 136.0938 Evaluate side-chains 254 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 520 VAL 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 262 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 0.0970 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN D 245 ASN D 434 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN D 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.148587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123904 restraints weight = 32096.430| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.76 r_work: 0.3804 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 1.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16212 Z= 0.152 Angle : 0.808 14.707 22044 Z= 0.375 Chirality : 0.046 0.830 2468 Planarity : 0.004 0.043 2708 Dihedral : 16.646 175.897 2400 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.54 % Allowed : 23.58 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.45 (0.19), residues: 1856 helix: 1.05 (0.17), residues: 948 sheet: -0.84 (0.42), residues: 164 loop : -2.01 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 322 TYR 0.017 0.001 TYR D 611 PHE 0.021 0.002 PHE A 506 TRP 0.050 0.002 TRP D 414 HIS 0.001 0.000 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (16196) covalent geometry : angle 0.78653 / 0.37 (22000) SS BOND : bond 0.00181 / 0.10 ( 4) SS BOND : angle 2.37245 / 1.21 ( 8) hydrogen bonds : bond 0.04115 / 2.61 ( 805) hydrogen bonds : angle 3.91554 / 2.68 ( 2463) link_NAG-ASN : bond 0.01053 / 0.72 ( 12) link_NAG-ASN : angle 4.53485 / 3.49 ( 36) *********************** 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: 77 poor density : 258 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.3341 (tm) REVERT: A 242 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6267 (tpp) REVERT: A 293 TRP cc_start: 0.7969 (m100) cc_final: 0.7160 (m100) REVERT: A 330 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 340 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: B 242 MET cc_start: 0.7240 (tpp) cc_final: 0.6772 (tpp) REVERT: B 273 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 312 GLU cc_start: 0.7995 (pt0) cc_final: 0.7734 (pt0) REVERT: B 353 GLU cc_start: 0.9111 (tt0) cc_final: 0.8885 (tp30) REVERT: B 503 PHE cc_start: 0.5142 (p90) cc_final: 0.4741 (m-10) REVERT: B 544 THR cc_start: 0.7769 (t) cc_final: 0.7461 (p) REVERT: B 595 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5392 (tmtt) REVERT: B 611 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 637 PHE cc_start: 0.8798 (m-80) cc_final: 0.7995 (m-80) REVERT: B 669 PHE cc_start: 0.6110 (p90) cc_final: 0.5851 (m-10) REVERT: B 670 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 675 MET cc_start: 0.5529 (mmp) cc_final: 0.5171 (mmp) REVERT: C 236 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 267 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7691 (mmtm) REVERT: C 278 ASP cc_start: 0.8245 (m-30) cc_final: 0.7827 (m-30) REVERT: C 517 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 648 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7601 (mt-10) REVERT: C 660 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5510 (t80) REVERT: C 675 MET cc_start: 0.6065 (mmm) cc_final: 0.5813 (mmp) REVERT: D 252 MET cc_start: 0.8346 (tmm) cc_final: 0.7585 (tpp) REVERT: D 295 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6336 (tmm) REVERT: D 344 CYS cc_start: 0.4597 (OUTLIER) cc_final: 0.3535 (t) REVERT: D 471 PHE cc_start: 0.6641 (m-80) cc_final: 0.5480 (t80) REVERT: D 485 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6829 (t80) REVERT: D 590 MET cc_start: 0.7300 (tpp) cc_final: 0.7059 (tpp) REVERT: D 593 CYS cc_start: 0.3188 (p) cc_final: 0.2884 (m) REVERT: D 631 GLU cc_start: 0.7607 (tt0) cc_final: 0.7366 (tm-30) REVERT: D 636 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8778 (mp10) REVERT: D 648 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7769 (mt-10) outliers start: 77 outliers final: 19 residues processed: 310 average time/residue: 0.3647 time to fit residues: 132.3627 Evaluate side-chains 247 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 636 GLN Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 430 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN B 578 ASN C 313 ASN C 559 ASN C 613 GLN C 636 GLN C 674 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 GLN D 578 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.147855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123051 restraints weight = 31859.578| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.78 r_work: 0.3798 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 1.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16212 Z= 0.136 Angle : 0.772 14.543 22044 Z= 0.357 Chirality : 0.042 0.161 2468 Planarity : 0.004 0.042 2708 Dihedral : 16.514 176.763 2400 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.07 % Allowed : 26.42 % Favored : 69.52 % 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: -0.37 (0.19), residues: 1856 helix: 1.06 (0.16), residues: 948 sheet: -0.38 (0.43), residues: 156 loop : -1.99 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 251 TYR 0.018 0.001 TYR B 348 PHE 0.027 0.002 PHE C 666 TRP 0.024 0.001 TRP D 414 HIS 0.002 0.000 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (16196) covalent geometry : angle 0.75034 / 0.35 (22000) SS BOND : bond 0.01255 / 0.64 ( 4) SS BOND : angle 2.10196 / 1.06 ( 8) hydrogen bonds : bond 0.03742 / 2.37 ( 805) hydrogen bonds : angle 3.89661 / 2.68 ( 2463) link_NAG-ASN : bond 0.00887 / 0.60 ( 12) link_NAG-ASN : angle 4.45191 / 3.46 ( 36) *********************** 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 305 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 TRP cc_start: 0.8120 (m100) cc_final: 0.7548 (m100) REVERT: A 314 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 603 MET cc_start: 0.7271 (tpp) cc_final: 0.7023 (tpt) REVERT: B 229 LEU cc_start: 0.8956 (mm) cc_final: 0.8740 (mp) REVERT: B 242 MET cc_start: 0.7753 (tpp) cc_final: 0.7317 (tpp) REVERT: B 273 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 312 GLU cc_start: 0.8112 (pt0) cc_final: 0.7619 (pm20) REVERT: B 353 GLU cc_start: 0.9095 (tt0) cc_final: 0.8864 (tp30) REVERT: B 482 PHE cc_start: 0.8856 (m-80) cc_final: 0.8306 (t80) REVERT: B 502 TYR cc_start: 0.7096 (t80) cc_final: 0.6640 (t80) REVERT: B 503 PHE cc_start: 0.5351 (p90) cc_final: 0.5016 (m-10) REVERT: B 544 THR cc_start: 0.7753 (t) cc_final: 0.7489 (p) REVERT: B 570 TRP cc_start: 0.8055 (m100) cc_final: 0.7805 (t-100) REVERT: B 595 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5711 (tmtt) REVERT: B 611 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8107 (t80) REVERT: B 637 PHE cc_start: 0.8894 (m-80) cc_final: 0.8112 (m-80) REVERT: B 650 GLU cc_start: 0.8303 (tt0) cc_final: 0.7776 (tp30) REVERT: B 669 PHE cc_start: 0.6234 (p90) cc_final: 0.5995 (m-10) REVERT: B 670 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 675 MET cc_start: 0.5587 (mmp) cc_final: 0.5307 (mmp) REVERT: C 236 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7784 (tp) REVERT: C 267 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7746 (mmtm) REVERT: C 278 ASP cc_start: 0.8359 (m-30) cc_final: 0.8064 (m-30) REVERT: C 517 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7026 (mp) REVERT: C 637 PHE cc_start: 0.8888 (m-80) cc_final: 0.8139 (m-80) REVERT: C 648 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7682 (mt-10) REVERT: C 660 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6630 (t80) REVERT: C 675 MET cc_start: 0.5801 (mmm) cc_final: 0.5600 (mmp) REVERT: D 252 MET cc_start: 0.8376 (tmm) cc_final: 0.7749 (tpp) REVERT: D 253 MET cc_start: 0.8865 (mmm) cc_final: 0.8422 (tpp) REVERT: D 255 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8743 (tm-30) REVERT: D 344 CYS cc_start: 0.3891 (OUTLIER) cc_final: 0.2965 (t) REVERT: D 346 ASP cc_start: 0.8017 (m-30) cc_final: 0.7514 (m-30) REVERT: D 471 PHE cc_start: 0.6721 (m-80) cc_final: 0.5606 (t80) REVERT: D 567 PHE cc_start: 0.6834 (t80) cc_final: 0.6612 (t80) REVERT: D 590 MET cc_start: 0.7356 (tpp) cc_final: 0.7117 (tpp) REVERT: D 593 CYS cc_start: 0.3563 (p) cc_final: 0.3148 (m) REVERT: D 637 PHE cc_start: 0.8764 (m-80) cc_final: 0.8145 (m-80) REVERT: D 648 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7909 (mt-10) REVERT: D 660 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7071 (t80) outliers start: 69 outliers final: 17 residues processed: 286 average time/residue: 0.3625 time to fit residues: 121.7046 Evaluate side-chains 240 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 589 THR 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 34 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN C 255 GLN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.140947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116238 restraints weight = 32050.425| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.69 r_work: 0.3728 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 1.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16212 Z= 0.149 Angle : 0.789 12.587 22044 Z= 0.369 Chirality : 0.043 0.219 2468 Planarity : 0.004 0.045 2708 Dihedral : 16.499 176.538 2400 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.30 % Allowed : 28.18 % Favored : 68.51 % 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: -0.42 (0.19), residues: 1856 helix: 0.97 (0.17), residues: 948 sheet: -0.32 (0.42), residues: 168 loop : -1.99 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 251 TYR 0.064 0.002 TYR A 611 PHE 0.028 0.002 PHE B 538 TRP 0.025 0.001 TRP A 366 HIS 0.002 0.000 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (16196) covalent geometry : angle 0.77204 / 0.36 (22000) SS BOND : bond 0.00298 / 0.15 ( 4) SS BOND : angle 2.15653 / 1.07 ( 8) hydrogen bonds : bond 0.03981 / 2.52 ( 805) hydrogen bonds : angle 3.93872 / 2.69 ( 2463) link_NAG-ASN : bond 0.00816 / 0.57 ( 12) link_NAG-ASN : angle 3.98948 / 3.09 ( 36) *********************** 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 280 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8500 (m-30) cc_final: 0.8088 (m-30) REVERT: A 293 TRP cc_start: 0.8296 (m100) cc_final: 0.8054 (m100) REVERT: A 295 MET cc_start: 0.4163 (tmm) cc_final: 0.3771 (tmm) REVERT: A 526 ILE cc_start: 0.8268 (tp) cc_final: 0.8067 (tp) REVERT: B 242 MET cc_start: 0.7973 (tpp) cc_final: 0.7759 (tpp) REVERT: B 312 GLU cc_start: 0.8175 (pt0) cc_final: 0.7958 (pt0) REVERT: B 353 GLU cc_start: 0.9125 (tt0) cc_final: 0.8876 (tp30) REVERT: B 502 TYR cc_start: 0.7140 (t80) cc_final: 0.6719 (t80) REVERT: B 503 PHE cc_start: 0.5419 (p90) cc_final: 0.4858 (m-10) REVERT: B 570 TRP cc_start: 0.8123 (m100) cc_final: 0.7700 (t-100) REVERT: B 595 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.5734 (tmtt) REVERT: B 611 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8063 (t80) REVERT: B 650 GLU cc_start: 0.8396 (tt0) cc_final: 0.7744 (tp30) REVERT: B 669 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.6095 (m-10) REVERT: B 670 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 675 MET cc_start: 0.5764 (mmp) cc_final: 0.5504 (mmp) REVERT: C 236 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 267 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7963 (mppt) REVERT: C 278 ASP cc_start: 0.8498 (m-30) cc_final: 0.8201 (m-30) REVERT: C 517 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7268 (mp) REVERT: C 573 LEU cc_start: 0.8935 (tt) cc_final: 0.8706 (pp) REVERT: C 648 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7835 (mt-10) REVERT: C 660 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 675 MET cc_start: 0.6243 (mmm) cc_final: 0.6037 (mmp) REVERT: D 252 MET cc_start: 0.8410 (tmm) cc_final: 0.7917 (tpp) REVERT: D 253 MET cc_start: 0.8977 (mmm) cc_final: 0.8690 (tpp) REVERT: D 278 ASP cc_start: 0.7614 (m-30) cc_final: 0.7182 (m-30) REVERT: D 344 CYS cc_start: 0.4792 (OUTLIER) cc_final: 0.3747 (t) REVERT: D 346 ASP cc_start: 0.8244 (m-30) cc_final: 0.7837 (m-30) REVERT: D 471 PHE cc_start: 0.6718 (m-80) cc_final: 0.5600 (t80) REVERT: D 593 CYS cc_start: 0.3881 (p) cc_final: 0.3296 (m) REVERT: D 611 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8131 (t80) REVERT: D 648 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8099 (mt-10) outliers start: 56 outliers final: 19 residues processed: 264 average time/residue: 0.3387 time to fit residues: 105.9175 Evaluate side-chains 220 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 425 ASP Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 456 GLN C 555 GLN C 559 ASN C 578 ASN D 245 ASN D 559 ASN D 578 ASN D 613 GLN D 636 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.125810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101880 restraints weight = 32924.946| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.56 r_work: 0.3482 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 1.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16212 Z= 0.246 Angle : 0.952 15.466 22044 Z= 0.460 Chirality : 0.049 0.203 2468 Planarity : 0.005 0.051 2708 Dihedral : 17.194 178.822 2400 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.95 % Allowed : 28.12 % Favored : 67.92 % 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: -1.03 (0.19), residues: 1856 helix: 0.48 (0.16), residues: 968 sheet: -1.03 (0.41), residues: 164 loop : -2.23 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 440 TYR 0.029 0.003 TYR C 345 PHE 0.033 0.003 PHE C 600 TRP 0.039 0.003 TRP A 366 HIS 0.003 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 (16196) covalent geometry : angle 0.93246 / 0.46 (22000) SS BOND : bond 0.00851 / 0.42 ( 4) SS BOND : angle 3.26449 / 1.53 ( 8) hydrogen bonds : bond 0.05787 / 3.68 ( 805) hydrogen bonds : angle 4.51787 / 3.06 ( 2463) link_NAG-ASN : bond 0.00956 / 0.58 ( 12) link_NAG-ASN : angle 4.63464 / 3.55 ( 36) *********************** 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 326 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8326 (tpp) cc_final: 0.8059 (mmt) REVERT: A 278 ASP cc_start: 0.8791 (m-30) cc_final: 0.8426 (m-30) REVERT: A 295 MET cc_start: 0.5718 (tmm) cc_final: 0.5489 (tmm) REVERT: A 442 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8980 (tm) REVERT: A 477 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7492 (tt0) REVERT: A 675 MET cc_start: 0.6866 (ppp) cc_final: 0.6477 (tpt) REVERT: A 681 ASN cc_start: 0.8682 (m-40) cc_final: 0.8148 (p0) REVERT: B 278 ASP cc_start: 0.8742 (m-30) cc_final: 0.8393 (m-30) REVERT: B 295 MET cc_start: 0.7005 (tpp) cc_final: 0.6641 (ttp) REVERT: B 312 GLU cc_start: 0.8438 (pt0) cc_final: 0.7833 (pm20) REVERT: B 502 TYR cc_start: 0.7465 (t80) cc_final: 0.7083 (t80) REVERT: B 507 TRP cc_start: 0.8668 (m100) cc_final: 0.8357 (m100) REVERT: B 595 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5545 (tmtt) REVERT: B 669 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6125 (m-10) REVERT: B 670 PHE cc_start: 0.7661 (t80) cc_final: 0.7432 (t80) REVERT: B 675 MET cc_start: 0.5935 (mmp) cc_final: 0.5522 (mmt) REVERT: C 236 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8019 (tp) REVERT: C 245 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7885 (t0) REVERT: C 278 ASP cc_start: 0.8623 (m-30) cc_final: 0.8292 (m-30) REVERT: C 502 TYR cc_start: 0.6315 (t80) cc_final: 0.4908 (t80) REVERT: C 583 MET cc_start: 0.0168 (mmp) cc_final: -0.0178 (mmm) REVERT: C 611 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7892 (t80) REVERT: C 648 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8156 (pt0) REVERT: C 669 PHE cc_start: 0.7489 (m-10) cc_final: 0.7188 (t80) REVERT: D 252 MET cc_start: 0.8542 (tmm) cc_final: 0.8245 (mpp) REVERT: D 278 ASP cc_start: 0.8267 (m-30) cc_final: 0.7880 (m-30) REVERT: D 281 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8523 (mtmt) REVERT: D 369 THR cc_start: 0.7654 (m) cc_final: 0.6732 (p) REVERT: D 471 PHE cc_start: 0.6839 (m-80) cc_final: 0.5665 (t80) REVERT: D 522 ILE cc_start: 0.8663 (tp) cc_final: 0.8424 (tt) REVERT: D 593 CYS cc_start: 0.4288 (p) cc_final: 0.3765 (m) REVERT: D 617 LEU cc_start: 0.9004 (tp) cc_final: 0.8652 (mm) REVERT: D 670 PHE cc_start: 0.7572 (t80) cc_final: 0.7263 (t80) outliers start: 67 outliers final: 22 residues processed: 308 average time/residue: 0.3764 time to fit residues: 134.9347 Evaluate side-chains 215 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 MET 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 442 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 233 VAL 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 472 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 245 ASN D 578 ASN D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100041 restraints weight = 32888.759| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.50 r_work: 0.3471 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 1.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16212 Z= 0.177 Angle : 0.892 13.285 22044 Z= 0.421 Chirality : 0.045 0.202 2468 Planarity : 0.004 0.043 2708 Dihedral : 17.032 179.533 2400 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.54 % Allowed : 32.61 % 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 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: -0.74 (0.19), residues: 1856 helix: 0.72 (0.16), residues: 972 sheet: -0.88 (0.43), residues: 164 loop : -2.11 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 251 TYR 0.029 0.002 TYR D 227 PHE 0.031 0.002 PHE B 485 TRP 0.026 0.002 TRP A 366 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (16196) covalent geometry : angle 0.87336 / 0.42 (22000) SS BOND : bond 0.01045 / 0.78 ( 4) SS BOND : angle 4.01319 / 1.88 ( 8) hydrogen bonds : bond 0.04590 / 2.91 ( 805) hydrogen bonds : angle 4.16841 / 2.83 ( 2463) link_NAG-ASN : bond 0.00814 / 0.50 ( 12) link_NAG-ASN : angle 4.22661 / 3.25 ( 36) *********************** 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 281 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8369 (tpp) cc_final: 0.8144 (mmt) REVERT: A 274 SER cc_start: 0.9385 (m) cc_final: 0.9008 (p) REVERT: A 477 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7749 (tt0) REVERT: A 527 TYR cc_start: 0.7619 (t80) cc_final: 0.7363 (t80) REVERT: A 542 GLN cc_start: 0.6160 (mp-120) cc_final: 0.5851 (mp-120) REVERT: A 675 MET cc_start: 0.6892 (ppp) cc_final: 0.6617 (tpt) REVERT: A 681 ASN cc_start: 0.8632 (m-40) cc_final: 0.8104 (p0) REVERT: B 278 ASP cc_start: 0.8720 (m-30) cc_final: 0.8429 (m-30) REVERT: B 295 MET cc_start: 0.6813 (tpp) cc_final: 0.6574 (ttp) REVERT: B 312 GLU cc_start: 0.8355 (pt0) cc_final: 0.8062 (pm20) REVERT: B 502 TYR cc_start: 0.7646 (t80) cc_final: 0.7327 (t80) REVERT: B 595 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5460 (tmtt) REVERT: B 603 MET cc_start: 0.8271 (tmm) cc_final: 0.8004 (tpt) REVERT: B 675 MET cc_start: 0.6119 (mmp) cc_final: 0.5684 (mmp) REVERT: C 239 TYR cc_start: 0.7836 (t80) cc_final: 0.7626 (t80) REVERT: C 278 ASP cc_start: 0.8501 (m-30) cc_final: 0.8251 (m-30) REVERT: C 531 ASN cc_start: 0.8090 (t0) cc_final: 0.6765 (m110) REVERT: C 583 MET cc_start: 0.0040 (mmp) cc_final: -0.0303 (mmm) REVERT: C 600 PHE cc_start: 0.6468 (m-80) cc_final: 0.5945 (m-80) REVERT: C 611 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7996 (t80) REVERT: C 669 PHE cc_start: 0.7482 (m-10) cc_final: 0.7252 (t80) REVERT: C 675 MET cc_start: 0.7389 (mmp) cc_final: 0.7123 (mmp) REVERT: D 252 MET cc_start: 0.8567 (tmm) cc_final: 0.8317 (tpp) REVERT: D 278 ASP cc_start: 0.8291 (m-30) cc_final: 0.8027 (m-30) REVERT: D 281 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8522 (mtmt) REVERT: D 312 GLU cc_start: 0.8309 (mp0) cc_final: 0.8091 (pm20) REVERT: D 364 THR cc_start: 0.7290 (p) cc_final: 0.7071 (p) REVERT: D 369 THR cc_start: 0.7785 (m) cc_final: 0.6896 (p) REVERT: D 401 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8792 (mp0) REVERT: D 477 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6559 (pp20) REVERT: D 506 PHE cc_start: 0.7061 (t80) cc_final: 0.6261 (p90) REVERT: D 522 ILE cc_start: 0.8837 (tp) cc_final: 0.8526 (tt) REVERT: D 611 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8159 (t80) REVERT: D 617 LEU cc_start: 0.8916 (tp) cc_final: 0.8632 (mm) REVERT: D 670 PHE cc_start: 0.7676 (t80) cc_final: 0.7360 (t80) REVERT: D 676 PHE cc_start: 0.8324 (t80) cc_final: 0.8030 (t80) outliers start: 43 outliers final: 21 residues processed: 264 average time/residue: 0.4162 time to fit residues: 127.2112 Evaluate side-chains 214 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 PHE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 157 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN D 578 ASN D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.123064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098399 restraints weight = 32971.284| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.62 r_work: 0.3419 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 1.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16212 Z= 0.154 Angle : 0.885 16.130 22044 Z= 0.416 Chirality : 0.044 0.205 2468 Planarity : 0.004 0.044 2708 Dihedral : 16.886 179.417 2400 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.59 % Allowed : 34.73 % Favored : 63.68 % 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: -0.64 (0.19), residues: 1856 helix: 0.93 (0.16), residues: 924 sheet: -0.75 (0.43), residues: 164 loop : -2.10 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 361 TYR 0.030 0.002 TYR C 348 PHE 0.033 0.002 PHE A 483 TRP 0.017 0.001 TRP D 414 HIS 0.001 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16196) covalent geometry : angle 0.86777 / 0.41 (22000) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 3.82984 / 1.87 ( 8) hydrogen bonds : bond 0.04232 / 2.71 ( 805) hydrogen bonds : angle 4.10230 / 2.77 ( 2463) link_NAG-ASN : bond 0.00806 / 0.50 ( 12) link_NAG-ASN : angle 4.02291 / 3.13 ( 36) ********************** 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 242 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.9286 (m) cc_final: 0.8890 (p) REVERT: A 341 ILE cc_start: 0.8497 (pp) cc_final: 0.8188 (mp) REVERT: A 342 LYS cc_start: 0.8924 (mppt) cc_final: 0.8540 (mmtt) REVERT: A 477 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7797 (tt0) REVERT: A 675 MET cc_start: 0.6880 (ppp) cc_final: 0.6629 (tpt) REVERT: A 681 ASN cc_start: 0.8601 (m-40) cc_final: 0.8082 (p0) REVERT: B 278 ASP cc_start: 0.8646 (m-30) cc_final: 0.8365 (m-30) REVERT: B 312 GLU cc_start: 0.8374 (pt0) cc_final: 0.7977 (pm20) REVERT: B 502 TYR cc_start: 0.7680 (t80) cc_final: 0.7428 (t80) REVERT: B 595 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5509 (tmtt) REVERT: B 611 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 675 MET cc_start: 0.6230 (mmp) cc_final: 0.5973 (mmp) REVERT: C 531 ASN cc_start: 0.8181 (t0) cc_final: 0.6930 (m110) REVERT: C 583 MET cc_start: 0.0400 (mmp) cc_final: 0.0125 (mmm) REVERT: C 592 ARG cc_start: 0.6525 (tmm160) cc_final: 0.6253 (tmm-80) REVERT: C 600 PHE cc_start: 0.6530 (m-80) cc_final: 0.5933 (m-80) REVERT: D 252 MET cc_start: 0.8485 (tmm) cc_final: 0.8130 (tpp) REVERT: D 277 GLU cc_start: 0.8538 (tp30) cc_final: 0.8171 (tp30) REVERT: D 278 ASP cc_start: 0.8260 (m-30) cc_final: 0.8046 (m-30) REVERT: D 281 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8268 (mtmt) REVERT: D 364 THR cc_start: 0.7274 (p) cc_final: 0.7049 (p) REVERT: D 369 THR cc_start: 0.7679 (m) cc_final: 0.6783 (p) REVERT: D 401 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8760 (mp0) REVERT: D 506 PHE cc_start: 0.7202 (t80) cc_final: 0.6534 (p90) REVERT: D 522 ILE cc_start: 0.8663 (tp) cc_final: 0.8407 (tt) REVERT: D 611 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8001 (t80) REVERT: D 670 PHE cc_start: 0.7640 (t80) cc_final: 0.7286 (t80) outliers start: 27 outliers final: 18 residues processed: 232 average time/residue: 0.3896 time to fit residues: 105.2677 Evaluate side-chains 219 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 242 MET 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 506 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 611 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 170 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 ASN A 559 ASN C 245 ASN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097767 restraints weight = 32931.368| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.59 r_work: 0.3408 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 1.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16212 Z= 0.155 Angle : 0.871 14.199 22044 Z= 0.410 Chirality : 0.044 0.198 2468 Planarity : 0.004 0.070 2708 Dihedral : 16.818 179.077 2400 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.12 % Allowed : 34.43 % Favored : 63.44 % 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: -0.64 (0.19), residues: 1856 helix: 0.90 (0.16), residues: 924 sheet: -0.70 (0.43), residues: 164 loop : -2.07 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 338 TYR 0.032 0.002 TYR C 502 PHE 0.037 0.002 PHE A 483 TRP 0.019 0.001 TRP D 414 HIS 0.001 0.000 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16196) covalent geometry : angle 0.85395 / 0.41 (22000) SS BOND : bond 0.00129 / 0.07 ( 4) SS BOND : angle 3.79846 / 1.86 ( 8) hydrogen bonds : bond 0.04214 / 2.70 ( 805) hydrogen bonds : angle 4.07164 / 2.75 ( 2463) link_NAG-ASN : bond 0.00755 / 0.48 ( 12) link_NAG-ASN : angle 3.95283 / 3.07 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.58 seconds wall clock time: 73 minutes 17.89 seconds (4397.89 seconds total)