Starting phenix.real_space_refine on Sat Jun 14 06:09:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk7_34848/06_2025/8hk7_34848_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 10428 2.51 5 N 2460 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' CA': 1, 'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.43, per 1000 atoms: 0.60 Number of scatterers: 15765 At special positions: 0 Unit cell: (108.7, 108.7, 102.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 80 16.00 O 2796 8.00 N 2460 7.00 C 10428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 328 " " NAG A1002 " - " ASN A 362 " " NAG A1003 " - " ASN A 375 " " NAG B1001 " - " ASN B 328 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 375 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 375 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 12 sheets defined 58.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 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: 4.71 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2408 1.30 - 1.43: 4742 1.43 - 1.56: 8915 1.56 - 1.68: 7 1.68 - 1.81: 124 Bond restraints: 16196 Sorted by residual: bond pdb=" C1 AQV A1005 " pdb=" C2 AQV A1005 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C1 AQV D1004 " pdb=" C2 AQV D1004 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C1 AQV C1004 " pdb=" C2 AQV C1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C1 AQV B1004 " pdb=" C2 AQV B1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C5 AQV A1005 " pdb=" C6 AQV A1005 " ideal model delta sigma weight residual 1.381 1.543 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 16191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 21400 2.02 - 4.04: 497 4.04 - 6.06: 72 6.06 - 8.08: 22 8.08 - 10.10: 9 Bond angle restraints: 22000 Sorted by residual: angle pdb=" N SER B 587 " pdb=" CA SER B 587 " pdb=" C SER B 587 " ideal model delta sigma weight residual 110.97 103.01 7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N SER A 587 " pdb=" CA SER A 587 " pdb=" C SER A 587 " ideal model delta sigma weight residual 110.80 102.00 8.80 2.13e+00 2.20e-01 1.71e+01 angle pdb=" N THR B 589 " pdb=" CA THR B 589 " pdb=" C THR B 589 " ideal model delta sigma weight residual 111.28 115.76 -4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" C PHE B 310 " pdb=" N TYR B 311 " pdb=" CA TYR B 311 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C PHE D 310 " pdb=" N TYR D 311 " pdb=" CA TYR D 311 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 21995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 9299 35.50 - 71.00: 191 71.00 - 106.50: 46 106.50 - 142.00: 4 142.00 - 177.49: 8 Dihedral angle restraints: 9548 sinusoidal: 4000 harmonic: 5548 Sorted by residual: dihedral pdb=" CA CYS C 331 " pdb=" C CYS C 331 " pdb=" N SER C 332 " pdb=" CA SER C 332 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA CYS D 331 " pdb=" C CYS D 331 " pdb=" N SER D 332 " pdb=" CA SER D 332 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA CYS B 331 " pdb=" C CYS B 331 " pdb=" N SER B 332 " pdb=" CA SER B 332 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1643 0.037 - 0.074: 574 0.074 - 0.110: 189 0.110 - 0.147: 52 0.147 - 0.184: 10 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA SER A 587 " pdb=" N SER A 587 " pdb=" C SER A 587 " pdb=" CB SER A 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA SER B 587 " pdb=" N SER B 587 " pdb=" C SER B 587 " pdb=" CB SER B 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA ARG B 592 " pdb=" N ARG B 592 " pdb=" C ARG B 592 " pdb=" CB ARG B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2465 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 585 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C GLN A 585 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN A 585 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 585 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLN C 585 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN C 585 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU C 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 585 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLN B 585 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 585 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 586 " 0.014 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 12 2.24 - 2.91: 6670 2.91 - 3.57: 22302 3.57 - 4.24: 34906 4.24 - 4.90: 62124 Nonbonded interactions: 126014 Sorted by model distance: nonbonded pdb=" CE1 TYR A 684 " pdb=" OH TYR D 684 " model vdw 1.579 3.340 nonbonded pdb=" O GLN D 585 " pdb=" CG2 THR D 589 " model vdw 1.990 3.460 nonbonded pdb=" OH TYR D 386 " pdb=" OE1 GLU D 444 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" OE1 GLU A 444 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" OE1 GLU B 444 " model vdw 2.203 3.040 ... (remaining 126009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'B' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'C' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'D' and (resid 215 through 688 or resid 1001 through 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.770 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.167 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 : 11.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 0.53 % Allowed : 0.88 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1856 helix: 0.45 (0.17), residues: 924 sheet: -1.09 (0.37), residues: 176 loop : -1.72 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS B 501 PHE 0.028 0.001 PHE C 483 TYR 0.023 0.001 TYR D 249 ARG 0.005 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.01581 ( 12) link_NAG-ASN : angle 8.50606 ( 36) hydrogen bonds : bond 0.16807 ( 805) hydrogen bonds : angle 5.76442 ( 2463) SS BOND : bond 0.00321 ( 4) SS BOND : angle 4.02232 ( 8) covalent geometry : bond 0.00914 (16196) covalent geometry : angle 0.74807 (22000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 458 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9245 time to fit residues: 486.3983 Evaluate side-chains 264 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain D residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.0050 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 167 optimal weight: 20.0000 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 585 GLN B 313 ASN B 531 ASN B 547 ASN B 636 GLN C 313 ASN C 323 GLN C 412 ASN C 456 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN C 674 ASN D 323 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 578 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.187423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.165711 restraints weight = 32439.867| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 4.00 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5107 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16212 Z= 0.158 Angle : 0.806 16.242 22044 Z= 0.383 Chirality : 0.043 0.178 2468 Planarity : 0.004 0.059 2708 Dihedral : 18.001 178.640 2402 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.42 % Allowed : 13.56 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1856 helix: 0.91 (0.17), residues: 960 sheet: -0.52 (0.41), residues: 176 loop : -1.60 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 280 HIS 0.002 0.000 HIS C 379 PHE 0.033 0.002 PHE B 669 TYR 0.026 0.002 TYR A 249 ARG 0.005 0.001 ARG C 322 Details of bonding type rmsd link_NAG-ASN : bond 0.01598 ( 12) link_NAG-ASN : angle 6.95774 ( 36) hydrogen bonds : bond 0.04365 ( 805) hydrogen bonds : angle 4.12400 ( 2463) SS BOND : bond 0.00964 ( 4) SS BOND : angle 3.14421 ( 8) covalent geometry : bond 0.00323 (16196) covalent geometry : angle 0.75369 (22000) *********************** 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 349 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5217 (tpp) REVERT: A 379 HIS cc_start: 0.4144 (OUTLIER) cc_final: 0.3577 (p-80) REVERT: A 439 VAL cc_start: 0.3294 (OUTLIER) cc_final: 0.2853 (p) REVERT: A 583 MET cc_start: 0.5533 (ppp) cc_final: 0.4869 (tpp) REVERT: B 235 CYS cc_start: 0.7218 (m) cc_final: 0.6932 (p) REVERT: B 348 TYR cc_start: 0.7991 (t80) cc_final: 0.7580 (t80) REVERT: B 445 PHE cc_start: 0.7687 (m-80) cc_final: 0.7188 (m-80) REVERT: B 482 PHE cc_start: 0.8669 (m-10) cc_final: 0.7910 (t80) REVERT: B 502 TYR cc_start: 0.6266 (t80) cc_final: 0.5310 (t80) REVERT: B 595 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4981 (tptm) REVERT: B 649 ILE cc_start: 0.7756 (mt) cc_final: 0.7390 (OUTLIER) REVERT: C 307 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7524 (t) REVERT: D 253 MET cc_start: 0.5062 (mmm) cc_final: 0.4831 (mmm) REVERT: D 259 ASP cc_start: 0.7518 (t0) cc_final: 0.7178 (t0) REVERT: D 471 PHE cc_start: 0.6410 (m-80) cc_final: 0.5449 (p90) outliers start: 58 outliers final: 25 residues processed: 324 average time/residue: 0.7519 time to fit residues: 285.4129 Evaluate side-chains 249 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 439 VAL 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 331 CYS Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 585 GLN B 412 ASN B 458 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 323 GLN D 379 HIS ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.176534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.153673 restraints weight = 32408.764| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.96 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 16212 Z= 0.212 Angle : 0.859 15.742 22044 Z= 0.413 Chirality : 0.043 0.188 2468 Planarity : 0.005 0.061 2708 Dihedral : 16.597 172.527 2400 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.25 % Allowed : 17.16 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1856 helix: 0.88 (0.17), residues: 956 sheet: -0.62 (0.42), residues: 176 loop : -1.73 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 280 HIS 0.002 0.001 HIS B 379 PHE 0.035 0.002 PHE B 485 TYR 0.020 0.002 TYR B 486 ARG 0.006 0.001 ARG D 251 Details of bonding type rmsd link_NAG-ASN : bond 0.01509 ( 12) link_NAG-ASN : angle 6.67858 ( 36) hydrogen bonds : bond 0.04531 ( 805) hydrogen bonds : angle 4.17236 ( 2463) SS BOND : bond 0.00398 ( 4) SS BOND : angle 2.71949 ( 8) covalent geometry : bond 0.00436 (16196) covalent geometry : angle 0.81463 (22000) *********************** 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 345 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 1.516 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 280 TRP cc_start: 0.5867 (OUTLIER) cc_final: 0.5439 (m-10) REVERT: A 346 ASP cc_start: 0.7476 (m-30) cc_final: 0.7207 (m-30) REVERT: A 507 TRP cc_start: 0.4745 (m100) cc_final: 0.3732 (p90) REVERT: A 583 MET cc_start: 0.5713 (ppp) cc_final: 0.5067 (ttt) REVERT: A 611 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 648 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7530 (mt-10) REVERT: B 440 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7848 (tpp80) REVERT: B 482 PHE cc_start: 0.8817 (m-10) cc_final: 0.8166 (t80) REVERT: B 595 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.5056 (tmtt) REVERT: B 640 ILE cc_start: 0.7809 (mm) cc_final: 0.7555 (mt) REVERT: C 309 ILE cc_start: 0.8484 (mt) cc_final: 0.8212 (mp) REVERT: C 676 PHE cc_start: 0.6873 (t80) cc_final: 0.6589 (t80) REVERT: D 245 ASN cc_start: 0.7637 (t0) cc_final: 0.7044 (p0) REVERT: D 310 PHE cc_start: 0.5531 (m-10) cc_final: 0.5256 (m-80) REVERT: D 312 GLU cc_start: 0.6847 (mp0) cc_final: 0.6644 (mp0) REVERT: D 435 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6629 (pt) REVERT: D 508 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6685 (p0) outliers start: 72 outliers final: 22 residues processed: 319 average time/residue: 0.7604 time to fit residues: 282.8440 Evaluate side-chains 248 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 439 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 666 PHE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 580 ASN 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 167 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN D 557 GLN D 636 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.166204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.142884 restraints weight = 32826.255| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.95 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.8616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16212 Z= 0.154 Angle : 0.822 14.643 22044 Z= 0.380 Chirality : 0.043 0.168 2468 Planarity : 0.004 0.050 2708 Dihedral : 16.498 176.662 2400 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.66 % Allowed : 20.22 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1856 helix: 0.73 (0.16), residues: 1004 sheet: -0.59 (0.43), residues: 164 loop : -1.78 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 414 HIS 0.010 0.001 HIS D 501 PHE 0.038 0.002 PHE B 485 TYR 0.019 0.001 TYR C 345 ARG 0.008 0.001 ARG C 592 Details of bonding type rmsd link_NAG-ASN : bond 0.01263 ( 12) link_NAG-ASN : angle 6.19560 ( 36) hydrogen bonds : bond 0.03987 ( 805) hydrogen bonds : angle 4.00078 ( 2463) SS BOND : bond 0.00245 ( 4) SS BOND : angle 2.21704 ( 8) covalent geometry : bond 0.00326 (16196) covalent geometry : angle 0.78302 (22000) *********************** 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 341 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 1.788 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: 0.5976 (OUTLIER) cc_final: 0.5469 (tpp) REVERT: A 252 MET cc_start: 0.7069 (tpt) cc_final: 0.6798 (tpp) REVERT: A 280 TRP cc_start: 0.6516 (OUTLIER) cc_final: 0.5727 (m-10) REVERT: A 335 GLN cc_start: 0.7596 (tp-100) cc_final: 0.6997 (mt0) REVERT: A 456 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7307 (pp30) REVERT: A 507 TRP cc_start: 0.5390 (m100) cc_final: 0.4147 (p90) REVERT: A 583 MET cc_start: 0.5752 (ppp) cc_final: 0.5228 (tpp) REVERT: A 611 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7753 (t80) REVERT: B 440 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8050 (tmm-80) REVERT: B 482 PHE cc_start: 0.8687 (m-10) cc_final: 0.8241 (t80) REVERT: B 586 LEU cc_start: 0.1365 (OUTLIER) cc_final: 0.1113 (tt) REVERT: B 595 LYS cc_start: 0.5474 (OUTLIER) cc_final: 0.5136 (tmtt) REVERT: B 640 ILE cc_start: 0.7959 (mm) cc_final: 0.7651 (mt) REVERT: C 236 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7469 (tp) REVERT: C 278 ASP cc_start: 0.7189 (m-30) cc_final: 0.6829 (m-30) REVERT: C 306 ARG cc_start: 0.7771 (mmt180) cc_final: 0.7171 (mmm-85) REVERT: C 335 GLN cc_start: 0.7662 (tp-100) cc_final: 0.6909 (tt0) REVERT: D 241 MET cc_start: 0.6339 (tmm) cc_final: 0.6025 (ttp) REVERT: D 245 ASN cc_start: 0.8161 (t0) cc_final: 0.7722 (p0) REVERT: D 295 MET cc_start: 0.5328 (ttp) cc_final: 0.5105 (tmm) REVERT: D 312 GLU cc_start: 0.7833 (mp0) cc_final: 0.7284 (mp0) REVERT: D 485 PHE cc_start: 0.6656 (m-80) cc_final: 0.6035 (t80) REVERT: D 539 LEU cc_start: 0.7347 (mm) cc_final: 0.6988 (tm) REVERT: D 660 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4471 (t80) outliers start: 79 outliers final: 17 residues processed: 317 average time/residue: 0.7807 time to fit residues: 290.0800 Evaluate side-chains 254 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 456 GLN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 580 ASN Chi-restraints excluded: chain D residue 589 THR 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 93 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 313 ASN A 323 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 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** C 456 GLN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.164303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.140378 restraints weight = 32873.129| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.98 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.9581 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= 0.144 Angle : 0.807 13.204 22044 Z= 0.371 Chirality : 0.043 0.210 2468 Planarity : 0.004 0.046 2708 Dihedral : 16.575 176.064 2400 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.89 % Allowed : 23.00 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1856 helix: 1.07 (0.17), residues: 948 sheet: -0.55 (0.43), residues: 164 loop : -1.85 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 455 HIS 0.003 0.000 HIS A 379 PHE 0.026 0.002 PHE B 669 TYR 0.022 0.001 TYR C 345 ARG 0.007 0.000 ARG A 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00994 ( 12) link_NAG-ASN : angle 5.08723 ( 36) hydrogen bonds : bond 0.03775 ( 805) hydrogen bonds : angle 3.93696 ( 2463) SS BOND : bond 0.00777 ( 4) SS BOND : angle 2.43736 ( 8) covalent geometry : bond 0.00305 (16196) covalent geometry : angle 0.78004 (22000) *********************** 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 315 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 249 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5748 (tpp) REVERT: A 269 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7520 (m-40) REVERT: A 276 MET cc_start: 0.6975 (ptt) cc_final: 0.6720 (ptp) REVERT: A 507 TRP cc_start: 0.5793 (m100) cc_final: 0.4588 (p90) REVERT: A 583 MET cc_start: 0.5608 (ppp) cc_final: 0.5274 (ttt) REVERT: A 606 ILE cc_start: 0.8348 (mm) cc_final: 0.8137 (mp) REVERT: A 611 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 440 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7953 (tmm-80) REVERT: B 595 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.5317 (tmtt) REVERT: B 611 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7605 (t80) REVERT: B 640 ILE cc_start: 0.8082 (mm) cc_final: 0.7849 (mt) REVERT: C 236 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7472 (tp) REVERT: C 242 MET cc_start: 0.7368 (tpp) cc_final: 0.7065 (tpp) REVERT: C 252 MET cc_start: 0.7840 (tmm) cc_final: 0.7539 (tpp) REVERT: C 278 ASP cc_start: 0.7533 (m-30) cc_final: 0.7115 (m-30) REVERT: C 306 ARG cc_start: 0.7775 (mmt180) cc_final: 0.7466 (mmt180) REVERT: C 335 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7224 (tt0) REVERT: C 592 ARG cc_start: 0.6593 (tmm160) cc_final: 0.6386 (tmm160) REVERT: D 241 MET cc_start: 0.6583 (tmm) cc_final: 0.6271 (ttp) REVERT: D 245 ASN cc_start: 0.7974 (t0) cc_final: 0.7684 (p0) REVERT: D 291 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7339 (pp) REVERT: D 293 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.5174 (m-90) REVERT: D 312 GLU cc_start: 0.7968 (mp0) cc_final: 0.7262 (mp0) REVERT: D 485 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6260 (t80) REVERT: D 608 PHE cc_start: 0.6604 (t80) cc_final: 0.6389 (t80) REVERT: D 653 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6220 (t0) outliers start: 66 outliers final: 23 residues processed: 289 average time/residue: 0.7629 time to fit residues: 259.0263 Evaluate side-chains 239 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 485 PHE 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 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 293 TRP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 344 CYS 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 653 ASN 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 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 155 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 456 GLN ** A 458 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 578 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN C 559 ASN D 456 GLN D 578 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.162995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.138089 restraints weight = 32939.224| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.98 r_work: 0.4005 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 1.0113 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= 0.139 Angle : 0.791 15.287 22044 Z= 0.364 Chirality : 0.042 0.157 2468 Planarity : 0.004 0.045 2708 Dihedral : 16.542 176.187 2400 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.42 % Allowed : 25.47 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1856 helix: 0.99 (0.17), residues: 948 sheet: 0.14 (0.45), residues: 144 loop : -1.90 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 455 HIS 0.001 0.000 HIS D 498 PHE 0.024 0.001 PHE B 669 TYR 0.015 0.001 TYR D 502 ARG 0.005 0.000 ARG A 338 Details of bonding type rmsd link_NAG-ASN : bond 0.01120 ( 12) link_NAG-ASN : angle 4.56014 ( 36) hydrogen bonds : bond 0.03720 ( 805) hydrogen bonds : angle 3.89612 ( 2463) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.79424 ( 8) covalent geometry : bond 0.00296 (16196) covalent geometry : angle 0.76926 (22000) *********************** 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 290 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LEU cc_start: 0.8635 (tp) cc_final: 0.7574 (tp) REVERT: A 507 TRP cc_start: 0.6143 (m100) cc_final: 0.4346 (p90) REVERT: A 583 MET cc_start: 0.5555 (ppp) cc_final: 0.5258 (ttt) REVERT: A 611 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 308 PHE cc_start: 0.7907 (m-10) cc_final: 0.7629 (m-10) REVERT: B 440 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8178 (tmm-80) REVERT: B 595 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5557 (tmtt) REVERT: B 640 ILE cc_start: 0.8109 (mm) cc_final: 0.7897 (OUTLIER) REVERT: B 669 PHE cc_start: 0.6153 (p90) cc_final: 0.5874 (m-10) REVERT: C 236 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7460 (tp) REVERT: C 242 MET cc_start: 0.7264 (tpp) cc_final: 0.6924 (tpp) REVERT: C 252 MET cc_start: 0.7957 (tmm) cc_final: 0.7672 (tpp) REVERT: C 278 ASP cc_start: 0.7733 (m-30) cc_final: 0.7304 (m-30) REVERT: C 306 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7519 (mmm-85) REVERT: C 335 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7202 (tt0) REVERT: C 666 PHE cc_start: 0.5003 (OUTLIER) cc_final: 0.4764 (m-10) REVERT: D 241 MET cc_start: 0.6403 (tmm) cc_final: 0.6059 (ttp) REVERT: D 291 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7299 (tp) REVERT: D 312 GLU cc_start: 0.8232 (mp0) cc_final: 0.7505 (mp0) REVERT: D 485 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6355 (t80) REVERT: D 539 LEU cc_start: 0.6942 (mm) cc_final: 0.6559 (tm) REVERT: D 578 ASN cc_start: 0.4475 (OUTLIER) cc_final: 0.4204 (t160) REVERT: D 608 PHE cc_start: 0.6831 (t80) cc_final: 0.6599 (t80) REVERT: D 653 ASN cc_start: 0.6858 (OUTLIER) cc_final: 0.6333 (t0) outliers start: 58 outliers final: 19 residues processed: 273 average time/residue: 0.7728 time to fit residues: 246.9897 Evaluate side-chains 233 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 666 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 653 ASN 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 92 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 GLN C 559 ASN C 578 ASN D 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.154173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129143 restraints weight = 32787.311| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.90 r_work: 0.3912 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 1.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16212 Z= 0.153 Angle : 0.828 14.845 22044 Z= 0.389 Chirality : 0.043 0.199 2468 Planarity : 0.004 0.044 2708 Dihedral : 16.462 175.871 2400 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 26.24 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1856 helix: 1.03 (0.17), residues: 936 sheet: 0.15 (0.44), residues: 144 loop : -1.97 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 455 HIS 0.002 0.000 HIS B 501 PHE 0.031 0.002 PHE B 538 TYR 0.023 0.001 TYR B 486 ARG 0.008 0.001 ARG D 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 12) link_NAG-ASN : angle 4.22637 ( 36) hydrogen bonds : bond 0.03984 ( 805) hydrogen bonds : angle 3.97381 ( 2463) SS BOND : bond 0.01582 ( 4) SS BOND : angle 3.57271 ( 8) covalent geometry : bond 0.00336 (16196) covalent geometry : angle 0.80845 (22000) *********************** 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 317 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7253 (mmt90) REVERT: A 439 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7588 (m) REVERT: A 507 TRP cc_start: 0.6669 (m100) cc_final: 0.4543 (p90) REVERT: A 583 MET cc_start: 0.5526 (ppp) cc_final: 0.5310 (ttt) REVERT: A 611 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8365 (t80) REVERT: A 637 PHE cc_start: 0.8791 (m-80) cc_final: 0.8247 (m-80) REVERT: A 669 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6408 (t80) REVERT: B 406 VAL cc_start: 0.8753 (t) cc_final: 0.8513 (m) REVERT: B 435 LEU cc_start: 0.9025 (tp) cc_final: 0.8709 (mt) REVERT: B 440 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (tmm-80) REVERT: B 595 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5979 (tmtt) REVERT: B 603 MET cc_start: 0.7757 (tmm) cc_final: 0.7134 (tpt) REVERT: B 669 PHE cc_start: 0.6052 (p90) cc_final: 0.5816 (m-10) REVERT: B 670 PHE cc_start: 0.7139 (t80) cc_final: 0.6821 (t80) REVERT: C 236 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7602 (tp) REVERT: C 242 MET cc_start: 0.7617 (tpp) cc_final: 0.7266 (tpp) REVERT: C 252 MET cc_start: 0.8249 (tmm) cc_final: 0.7995 (tpp) REVERT: C 253 MET cc_start: 0.9081 (mmm) cc_final: 0.8783 (tpp) REVERT: C 259 ASP cc_start: 0.8797 (m-30) cc_final: 0.8534 (m-30) REVERT: C 278 ASP cc_start: 0.8162 (m-30) cc_final: 0.7735 (m-30) REVERT: C 306 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7470 (mmm-85) REVERT: C 335 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7574 (tt0) REVERT: C 675 MET cc_start: 0.5736 (mmm) cc_final: 0.5512 (mmp) REVERT: D 241 MET cc_start: 0.6963 (tmm) cc_final: 0.6711 (ttp) REVERT: D 276 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7350 (ptp) REVERT: D 312 GLU cc_start: 0.8322 (mp0) cc_final: 0.8077 (mp0) REVERT: D 471 PHE cc_start: 0.6646 (m-80) cc_final: 0.5313 (t80) REVERT: D 485 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6639 (t80) REVERT: D 633 ILE cc_start: 0.8122 (mm) cc_final: 0.7771 (mm) REVERT: D 637 PHE cc_start: 0.8658 (m-80) cc_final: 0.8195 (m-80) outliers start: 59 outliers final: 19 residues processed: 295 average time/residue: 0.7822 time to fit residues: 269.4093 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 : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 580 ASN Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 124 optimal weight: 9.9990 chunk 13 optimal weight: 0.0170 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN C 456 GLN C 674 ASN D 245 ASN D 255 GLN D 434 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.147928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122434 restraints weight = 32212.867| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.98 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 1.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 16212 Z= 0.167 Angle : 0.871 15.958 22044 Z= 0.408 Chirality : 0.045 0.189 2468 Planarity : 0.004 0.048 2708 Dihedral : 16.508 176.117 2400 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.07 % Allowed : 28.07 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1856 helix: 0.91 (0.17), residues: 936 sheet: 0.37 (0.44), residues: 148 loop : -1.95 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 280 HIS 0.009 0.001 HIS D 550 PHE 0.046 0.002 PHE B 483 TYR 0.026 0.002 TYR A 348 ARG 0.012 0.001 ARG D 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 12) link_NAG-ASN : angle 3.92783 ( 36) hydrogen bonds : bond 0.04287 ( 805) hydrogen bonds : angle 4.08059 ( 2463) SS BOND : bond 0.00587 ( 4) SS BOND : angle 3.10649 ( 8) covalent geometry : bond 0.00372 (16196) covalent geometry : angle 0.85510 (22000) *********************** 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 313 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8447 (m-30) cc_final: 0.8023 (m-30) REVERT: A 295 MET cc_start: 0.4397 (tmm) cc_final: 0.4131 (tmm) REVERT: A 338 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7369 (mmt90) REVERT: A 401 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8510 (mp0) REVERT: A 605 PHE cc_start: 0.8373 (t80) cc_final: 0.8058 (t80) REVERT: B 242 MET cc_start: 0.7533 (tpt) cc_final: 0.7298 (tpp) REVERT: B 502 TYR cc_start: 0.6735 (t80) cc_final: 0.6339 (t80) REVERT: B 544 THR cc_start: 0.7787 (t) cc_final: 0.7552 (p) REVERT: B 595 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.6019 (tmtt) REVERT: B 603 MET cc_start: 0.7808 (tmm) cc_final: 0.7145 (tpt) REVERT: B 670 PHE cc_start: 0.7153 (t80) cc_final: 0.6768 (t80) REVERT: C 236 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (tp) REVERT: C 242 MET cc_start: 0.7943 (tpp) cc_final: 0.7429 (tpp) REVERT: C 253 MET cc_start: 0.8816 (mmm) cc_final: 0.8558 (tpp) REVERT: C 259 ASP cc_start: 0.8648 (m-30) cc_final: 0.8317 (m-30) REVERT: C 278 ASP cc_start: 0.8234 (m-30) cc_final: 0.7768 (m-30) REVERT: C 348 TYR cc_start: 0.8584 (t80) cc_final: 0.8298 (t80) REVERT: C 414 TRP cc_start: 0.9203 (OUTLIER) cc_final: 0.8988 (t60) REVERT: C 531 ASN cc_start: 0.7813 (t0) cc_final: 0.6554 (m110) REVERT: C 675 MET cc_start: 0.6047 (mmm) cc_final: 0.5753 (mmp) REVERT: D 278 ASP cc_start: 0.7152 (m-30) cc_final: 0.6693 (m-30) REVERT: D 312 GLU cc_start: 0.7910 (mp0) cc_final: 0.7579 (mp0) REVERT: D 414 TRP cc_start: 0.7609 (OUTLIER) cc_final: 0.6673 (t60) REVERT: D 471 PHE cc_start: 0.6536 (m-80) cc_final: 0.5349 (t80) REVERT: D 611 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8210 (t80) REVERT: D 648 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7830 (mt-10) outliers start: 52 outliers final: 15 residues processed: 298 average time/residue: 0.7962 time to fit residues: 277.9828 Evaluate side-chains 223 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 414 TRP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN C 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.135422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.110741 restraints weight = 32409.053| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.85 r_work: 0.3600 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 1.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16212 Z= 0.199 Angle : 0.941 13.225 22044 Z= 0.453 Chirality : 0.048 0.218 2468 Planarity : 0.005 0.057 2708 Dihedral : 16.727 176.025 2400 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.14 % Favored : 91.81 % Rotamer: Outliers : 2.18 % Allowed : 31.90 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1856 helix: 0.51 (0.16), residues: 964 sheet: -0.68 (0.42), residues: 164 loop : -1.94 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 455 HIS 0.002 0.001 HIS D 498 PHE 0.038 0.003 PHE B 538 TYR 0.024 0.002 TYR C 611 ARG 0.008 0.001 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 12) link_NAG-ASN : angle 4.05362 ( 36) hydrogen bonds : bond 0.05090 ( 805) hydrogen bonds : angle 4.32891 ( 2463) SS BOND : bond 0.00677 ( 4) SS BOND : angle 2.42467 ( 8) covalent geometry : bond 0.00455 (16196) covalent geometry : angle 0.92668 (22000) *********************** 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 278 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8668 (m-30) cc_final: 0.8364 (m-30) REVERT: A 602 ILE cc_start: 0.8242 (pt) cc_final: 0.8004 (pp) REVERT: A 605 PHE cc_start: 0.8430 (t80) cc_final: 0.8154 (t80) REVERT: A 681 ASN cc_start: 0.8713 (m-40) cc_final: 0.8190 (p0) REVERT: B 295 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.4850 (mtp) REVERT: B 595 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5822 (tmtt) REVERT: C 245 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7704 (t0) REVERT: C 259 ASP cc_start: 0.8828 (m-30) cc_final: 0.8475 (m-30) REVERT: C 267 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8120 (mmtm) REVERT: C 277 GLU cc_start: 0.8443 (tp30) cc_final: 0.8235 (tp30) REVERT: C 278 ASP cc_start: 0.8583 (m-30) cc_final: 0.8220 (m-30) REVERT: C 414 TRP cc_start: 0.9273 (OUTLIER) cc_final: 0.8993 (t60) REVERT: C 518 SER cc_start: 0.9114 (m) cc_final: 0.8899 (m) REVERT: C 531 ASN cc_start: 0.8062 (t0) cc_final: 0.6775 (m110) REVERT: C 592 ARG cc_start: 0.6184 (tmm160) cc_final: 0.5594 (tmm-80) REVERT: C 660 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8131 (t80) REVERT: D 277 GLU cc_start: 0.8656 (tp30) cc_final: 0.8435 (tp30) REVERT: D 278 ASP cc_start: 0.8225 (m-30) cc_final: 0.7844 (m-30) REVERT: D 293 TRP cc_start: 0.7644 (m-90) cc_final: 0.7213 (m100) REVERT: D 312 GLU cc_start: 0.8374 (mp0) cc_final: 0.8088 (mp0) REVERT: D 401 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8691 (mp0) REVERT: D 572 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7916 (ttpt) REVERT: D 628 THR cc_start: 0.8541 (m) cc_final: 0.8246 (p) outliers start: 37 outliers final: 14 residues processed: 264 average time/residue: 0.7860 time to fit residues: 242.4856 Evaluate side-chains 209 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 572 LYS Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 128 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 180 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 412 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 GLN D 412 ASN D 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.139225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.114562 restraints weight = 32204.900| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.88 r_work: 0.3633 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 1.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16212 Z= 0.155 Angle : 0.906 16.176 22044 Z= 0.424 Chirality : 0.045 0.213 2468 Planarity : 0.004 0.042 2708 Dihedral : 16.558 177.771 2400 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.47 % Allowed : 34.14 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1856 helix: 0.65 (0.16), residues: 968 sheet: -0.01 (0.45), residues: 144 loop : -2.06 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 366 HIS 0.002 0.000 HIS C 501 PHE 0.041 0.002 PHE B 634 TYR 0.029 0.001 TYR B 239 ARG 0.009 0.001 ARG D 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 12) link_NAG-ASN : angle 3.61151 ( 36) hydrogen bonds : bond 0.04125 ( 805) hydrogen bonds : angle 4.13331 ( 2463) SS BOND : bond 0.00703 ( 4) SS BOND : angle 2.99359 ( 8) covalent geometry : bond 0.00340 (16196) covalent geometry : angle 0.89313 (22000) ********************** 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 269 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8577 (m-30) cc_final: 0.8300 (m-30) REVERT: A 342 LYS cc_start: 0.8805 (mppt) cc_final: 0.8345 (mmtt) REVERT: A 605 PHE cc_start: 0.8425 (t80) cc_final: 0.8164 (t80) REVERT: A 675 MET cc_start: 0.7046 (ppp) cc_final: 0.6367 (tpt) REVERT: A 681 ASN cc_start: 0.8695 (m-40) cc_final: 0.8116 (p0) REVERT: B 242 MET cc_start: 0.7991 (tpp) cc_final: 0.7682 (tpp) REVERT: B 294 LYS cc_start: 0.7101 (tppt) cc_final: 0.6321 (pmmt) REVERT: B 295 MET cc_start: 0.5340 (OUTLIER) cc_final: 0.4324 (mtp) REVERT: B 595 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.5963 (tmtt) REVERT: B 603 MET cc_start: 0.7959 (tmm) cc_final: 0.7439 (tpt) REVERT: C 245 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7787 (t0) REVERT: C 259 ASP cc_start: 0.8633 (m-30) cc_final: 0.8306 (m-30) REVERT: C 267 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8082 (mmtm) REVERT: C 278 ASP cc_start: 0.8515 (m-30) cc_final: 0.8283 (m-30) REVERT: C 414 TRP cc_start: 0.9153 (OUTLIER) cc_final: 0.8938 (t60) REVERT: C 531 ASN cc_start: 0.7822 (t0) cc_final: 0.6496 (m110) REVERT: C 592 ARG cc_start: 0.6334 (tmm160) cc_final: 0.5956 (tmm-80) REVERT: C 600 PHE cc_start: 0.6699 (m-80) cc_final: 0.6475 (m-80) REVERT: C 669 PHE cc_start: 0.7042 (m-10) cc_final: 0.6582 (t80) REVERT: C 670 PHE cc_start: 0.7622 (t80) cc_final: 0.7410 (t80) REVERT: D 259 ASP cc_start: 0.8795 (m-30) cc_final: 0.8203 (m-30) REVERT: D 277 GLU cc_start: 0.8518 (tp30) cc_final: 0.8307 (tp30) REVERT: D 278 ASP cc_start: 0.7995 (m-30) cc_final: 0.7784 (m-30) REVERT: D 293 TRP cc_start: 0.7640 (m-90) cc_final: 0.7361 (m-90) REVERT: D 312 GLU cc_start: 0.8212 (mp0) cc_final: 0.7929 (mp0) REVERT: D 506 PHE cc_start: 0.6841 (t80) cc_final: 0.6002 (p90) REVERT: D 628 THR cc_start: 0.8259 (m) cc_final: 0.8044 (p) REVERT: D 650 GLU cc_start: 0.8440 (pp20) cc_final: 0.7882 (pm20) outliers start: 25 outliers final: 8 residues processed: 258 average time/residue: 0.8308 time to fit residues: 248.5929 Evaluate side-chains 211 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111096 restraints weight = 32295.787| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.81 r_work: 0.3655 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 1.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16212 Z= 0.155 Angle : 0.912 14.886 22044 Z= 0.427 Chirality : 0.045 0.207 2468 Planarity : 0.005 0.123 2708 Dihedral : 16.521 177.371 2400 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.42 % Allowed : 35.38 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1856 helix: 0.75 (0.16), residues: 944 sheet: 0.10 (0.45), residues: 144 loop : -2.10 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 455 HIS 0.002 0.000 HIS D 550 PHE 0.041 0.002 PHE B 634 TYR 0.029 0.001 TYR C 239 ARG 0.013 0.001 ARG A 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 12) link_NAG-ASN : angle 3.41154 ( 36) hydrogen bonds : bond 0.04058 ( 805) hydrogen bonds : angle 4.06983 ( 2463) SS BOND : bond 0.00364 ( 4) SS BOND : angle 2.73612 ( 8) covalent geometry : bond 0.00345 (16196) covalent geometry : angle 0.90092 (22000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.61 seconds wall clock time: 145 minutes 34.82 seconds (8734.82 seconds total)