Starting phenix.real_space_refine on Sun Aug 24 00:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk7_34848/08_2025/8hk7_34848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk7_34848/08_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_34848/08_2025/8hk7_34848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk7_34848/08_2025/8hk7_34848.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk7_34848/08_2025/8hk7_34848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk7_34848/08_2025/8hk7_34848_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 10428 2.51 5 N 2460 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 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: 3.12, per 1000 atoms: 0.20 Number of scatterers: 15765 At special positions: 0 Unit cell: (108.7, 108.7, 102.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 80 16.00 O 2796 8.00 N 2460 7.00 C 10428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 328 " " NAG A1002 " - " ASN A 362 " " NAG A1003 " - " ASN A 375 " " NAG B1001 " - " ASN B 328 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 375 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 375 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 536.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 12 sheets defined 58.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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: 2.27 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2408 1.30 - 1.43: 4742 1.43 - 1.56: 8915 1.56 - 1.68: 7 1.68 - 1.81: 124 Bond restraints: 16196 Sorted by residual: bond pdb=" C1 AQV A1005 " pdb=" C2 AQV A1005 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C1 AQV D1004 " pdb=" C2 AQV D1004 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C1 AQV C1004 " pdb=" C2 AQV C1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C1 AQV B1004 " pdb=" C2 AQV B1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C5 AQV A1005 " pdb=" C6 AQV A1005 " ideal model delta sigma weight residual 1.381 1.543 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 16191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 21400 2.02 - 4.04: 497 4.04 - 6.06: 72 6.06 - 8.08: 22 8.08 - 10.10: 9 Bond angle restraints: 22000 Sorted by residual: angle pdb=" N SER B 587 " pdb=" CA SER B 587 " pdb=" C SER B 587 " ideal model delta sigma weight residual 110.97 103.01 7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N SER A 587 " pdb=" CA SER A 587 " pdb=" C SER A 587 " ideal model delta sigma weight residual 110.80 102.00 8.80 2.13e+00 2.20e-01 1.71e+01 angle pdb=" N THR B 589 " pdb=" CA THR B 589 " pdb=" C THR B 589 " ideal model delta sigma weight residual 111.28 115.76 -4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" C PHE B 310 " pdb=" N TYR B 311 " pdb=" CA TYR B 311 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C PHE D 310 " pdb=" N TYR D 311 " pdb=" CA TYR D 311 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 21995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 9299 35.50 - 71.00: 191 71.00 - 106.50: 46 106.50 - 142.00: 4 142.00 - 177.49: 8 Dihedral angle restraints: 9548 sinusoidal: 4000 harmonic: 5548 Sorted by residual: dihedral pdb=" CA CYS C 331 " pdb=" C CYS C 331 " pdb=" N SER C 332 " pdb=" CA SER C 332 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA CYS D 331 " pdb=" C CYS D 331 " pdb=" N SER D 332 " pdb=" CA SER D 332 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA CYS B 331 " pdb=" C CYS B 331 " pdb=" N SER B 332 " pdb=" CA SER B 332 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1643 0.037 - 0.074: 574 0.074 - 0.110: 189 0.110 - 0.147: 52 0.147 - 0.184: 10 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA SER A 587 " pdb=" N SER A 587 " pdb=" C SER A 587 " pdb=" CB SER A 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA SER B 587 " pdb=" N SER B 587 " pdb=" C SER B 587 " pdb=" CB SER B 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA ARG B 592 " pdb=" N ARG B 592 " pdb=" C ARG B 592 " pdb=" CB ARG B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2465 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 585 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C GLN A 585 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN A 585 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 585 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLN C 585 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN C 585 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU C 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 585 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLN B 585 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 585 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 586 " 0.014 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 12 2.24 - 2.91: 6670 2.91 - 3.57: 22302 3.57 - 4.24: 34906 4.24 - 4.90: 62124 Nonbonded interactions: 126014 Sorted by model distance: nonbonded pdb=" CE1 TYR A 684 " pdb=" OH TYR D 684 " model vdw 1.579 3.340 nonbonded pdb=" O GLN D 585 " pdb=" CG2 THR D 589 " model vdw 1.990 3.460 nonbonded pdb=" OH TYR D 386 " pdb=" OE1 GLU D 444 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" OE1 GLU A 444 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" OE1 GLU B 444 " model vdw 2.203 3.040 ... (remaining 126009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 215 through 1003) selection = (chain 'B' and resid 215 through 1003) selection = (chain 'C' and resid 215 through 1003) selection = (chain 'D' and resid 215 through 1003) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- 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 : 11.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 0.53 % Allowed : 0.88 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.20), residues: 1856 helix: 0.45 (0.17), residues: 924 sheet: -1.09 (0.37), residues: 176 loop : -1.72 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.023 0.001 TYR D 249 PHE 0.028 0.001 PHE C 483 TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00914 (16196) covalent geometry : angle 0.74807 (22000) SS BOND : bond 0.00321 ( 4) SS BOND : angle 4.02232 ( 8) hydrogen bonds : bond 0.16807 ( 805) hydrogen bonds : angle 5.76442 ( 2463) link_NAG-ASN : bond 0.01581 ( 12) link_NAG-ASN : angle 8.50606 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 458 time to evaluate : 0.471 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: 0.2513 (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: 0.3705 time to fit residues: 194.8137 Evaluate side-chains 265 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain D residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 379 HIS A 458 GLN A 508 ASN A 578 ASN A 585 GLN B 313 ASN B 412 ASN B 456 GLN B 531 ASN B 547 ASN B 636 GLN C 313 ASN C 323 GLN C 412 ASN C 613 GLN C 636 GLN C 674 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 HIS D 501 HIS D 578 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.170537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.147530 restraints weight = 32860.976| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 4.03 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.7818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16212 Z= 0.262 Angle : 0.990 17.276 22044 Z= 0.491 Chirality : 0.051 0.200 2468 Planarity : 0.007 0.094 2708 Dihedral : 18.081 164.864 2402 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.60 % Favored : 92.35 % Rotamer: Outliers : 5.01 % Allowed : 13.68 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.19), residues: 1856 helix: 0.22 (0.16), residues: 940 sheet: -0.71 (0.42), residues: 164 loop : -1.96 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 222 TYR 0.027 0.003 TYR D 502 PHE 0.051 0.003 PHE C 664 TRP 0.031 0.002 TRP A 293 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00521 (16196) covalent geometry : angle 0.94493 (22000) SS BOND : bond 0.02284 ( 4) SS BOND : angle 4.49108 ( 8) hydrogen bonds : bond 0.05831 ( 805) hydrogen bonds : angle 4.90156 ( 2463) link_NAG-ASN : bond 0.01836 ( 12) link_NAG-ASN : angle 7.03542 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 321 time to evaluate : 0.598 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 242 MET cc_start: 0.6501 (ptm) cc_final: 0.5579 (tpp) REVERT: A 280 TRP cc_start: 0.6490 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: A 379 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4428 (p-80) REVERT: A 507 TRP cc_start: 0.5549 (m100) cc_final: 0.3833 (p90) REVERT: A 583 MET cc_start: 0.5767 (ppp) cc_final: 0.5184 (ttt) REVERT: A 613 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7396 (tp-100) REVERT: B 348 TYR cc_start: 0.8789 (t80) cc_final: 0.7993 (t80) REVERT: B 406 VAL cc_start: 0.8815 (t) cc_final: 0.8555 (m) REVERT: B 435 LEU cc_start: 0.8779 (tp) cc_final: 0.8527 (tt) REVERT: B 440 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7807 (tmm-80) REVERT: B 482 PHE cc_start: 0.8750 (m-10) cc_final: 0.8164 (t80) REVERT: B 595 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4778 (tttt) REVERT: C 236 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (tp) REVERT: C 307 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.7832 (t) REVERT: C 414 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.8168 (t60) REVERT: C 448 THR cc_start: 0.7495 (p) cc_final: 0.6836 (p) REVERT: D 295 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.4329 (tmm) REVERT: D 314 LEU cc_start: 0.3859 (OUTLIER) cc_final: 0.2996 (tt) REVERT: D 315 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5372 (tt) REVERT: D 484 ILE cc_start: 0.4646 (OUTLIER) cc_final: 0.4412 (pt) REVERT: D 592 ARG cc_start: 0.7670 (mmt180) cc_final: 0.7044 (mmm160) outliers start: 85 outliers final: 19 residues processed: 378 average time/residue: 0.3234 time to fit residues: 141.3638 Evaluate side-chains 249 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 326 VAL 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 571 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 539 LEU 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: 0.2980 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 3 optimal weight: 0.0060 chunk 1 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 458 GLN B 559 ASN C 559 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.167898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.144112 restraints weight = 32888.255| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.91 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.8717 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= 0.143 Angle : 0.796 16.983 22044 Z= 0.371 Chirality : 0.042 0.159 2468 Planarity : 0.004 0.054 2708 Dihedral : 17.055 177.536 2400 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.13 % Allowed : 19.28 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.20), residues: 1856 helix: 1.03 (0.17), residues: 940 sheet: -0.66 (0.42), residues: 164 loop : -1.97 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 397 TYR 0.015 0.001 TYR B 249 PHE 0.022 0.002 PHE D 574 TRP 0.029 0.001 TRP D 414 HIS 0.003 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00298 (16196) covalent geometry : angle 0.74284 (22000) SS BOND : bond 0.00340 ( 4) SS BOND : angle 2.47039 ( 8) hydrogen bonds : bond 0.04164 ( 805) hydrogen bonds : angle 4.06146 ( 2463) link_NAG-ASN : bond 0.01443 ( 12) link_NAG-ASN : angle 7.03543 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5573 (tpp) REVERT: A 280 TRP cc_start: 0.6566 (OUTLIER) cc_final: 0.5804 (m-10) REVERT: A 335 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7075 (mt0) REVERT: A 507 TRP cc_start: 0.5373 (m100) cc_final: 0.4002 (p90) REVERT: A 583 MET cc_start: 0.5859 (ppp) cc_final: 0.5392 (ttt) REVERT: A 585 GLN cc_start: -0.1424 (OUTLIER) cc_final: -0.1993 (pt0) REVERT: A 668 MET cc_start: 0.5234 (pp-130) cc_final: 0.4634 (pp-130) REVERT: B 242 MET cc_start: 0.6993 (tpt) cc_final: 0.6693 (tpp) REVERT: B 312 GLU cc_start: 0.7154 (pt0) cc_final: 0.6950 (pm20) REVERT: B 353 GLU cc_start: 0.8493 (tt0) cc_final: 0.8228 (tt0) REVERT: B 482 PHE cc_start: 0.8725 (m-10) cc_final: 0.8187 (t80) REVERT: B 502 TYR cc_start: 0.7143 (t80) cc_final: 0.5400 (t80) REVERT: B 595 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4899 (tttt) REVERT: B 605 PHE cc_start: 0.8140 (t80) cc_final: 0.7865 (t80) REVERT: C 236 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7584 (tp) REVERT: C 278 ASP cc_start: 0.7286 (m-30) cc_final: 0.6934 (m-30) REVERT: C 312 GLU cc_start: 0.7719 (pt0) cc_final: 0.7507 (pt0) REVERT: C 522 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 666 PHE cc_start: 0.4495 (m-80) cc_final: 0.4029 (m-10) REVERT: D 295 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4577 (tmm) REVERT: D 314 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4313 (tt) REVERT: D 456 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7919 (pp30) REVERT: D 485 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5819 (t80) REVERT: D 593 CYS cc_start: 0.2496 (p) cc_final: 0.2252 (m) REVERT: D 653 ASN cc_start: 0.6505 (t0) cc_final: 0.6173 (t0) outliers start: 70 outliers final: 12 residues processed: 309 average time/residue: 0.2915 time to fit residues: 105.3699 Evaluate side-chains 246 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 379 HIS Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN C 547 ASN C 555 GLN C 559 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127582 restraints weight = 32471.690| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.96 r_work: 0.3787 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 1.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16212 Z= 0.167 Angle : 0.826 16.063 22044 Z= 0.386 Chirality : 0.045 0.281 2468 Planarity : 0.004 0.043 2708 Dihedral : 16.545 175.709 2400 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.25 % Allowed : 21.23 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1856 helix: 1.12 (0.17), residues: 940 sheet: -0.96 (0.40), residues: 176 loop : -1.91 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 581 TYR 0.017 0.002 TYR A 429 PHE 0.024 0.002 PHE B 426 TRP 0.025 0.002 TRP D 414 HIS 0.005 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00356 (16196) covalent geometry : angle 0.78017 (22000) SS BOND : bond 0.01313 ( 4) SS BOND : angle 2.66892 ( 8) hydrogen bonds : bond 0.04418 ( 805) hydrogen bonds : angle 3.97871 ( 2463) link_NAG-ASN : bond 0.01268 ( 12) link_NAG-ASN : angle 6.67699 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3207 (OUTLIER) cc_final: 0.2984 (tm) REVERT: A 242 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.5981 (tpp) REVERT: A 252 MET cc_start: 0.7642 (tpt) cc_final: 0.7439 (tpt) REVERT: A 335 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7628 (mt0) REVERT: A 507 TRP cc_start: 0.6589 (m100) cc_final: 0.4532 (p90) REVERT: A 583 MET cc_start: 0.5367 (ppp) cc_final: 0.5159 (tpp) REVERT: A 585 GLN cc_start: -0.0206 (OUTLIER) cc_final: -0.0517 (pt0) REVERT: A 609 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 242 MET cc_start: 0.7428 (tpt) cc_final: 0.7130 (tpp) REVERT: B 312 GLU cc_start: 0.7700 (pt0) cc_final: 0.7483 (pt0) REVERT: B 406 VAL cc_start: 0.8576 (t) cc_final: 0.8340 (m) REVERT: B 482 PHE cc_start: 0.8711 (m-10) cc_final: 0.8339 (t80) REVERT: B 502 TYR cc_start: 0.6425 (t80) cc_final: 0.6080 (t80) REVERT: B 503 PHE cc_start: 0.5301 (p90) cc_final: 0.5074 (m-10) REVERT: B 595 LYS cc_start: 0.5568 (OUTLIER) cc_final: 0.5252 (tmtt) REVERT: B 669 PHE cc_start: 0.6277 (p90) cc_final: 0.5782 (m-10) REVERT: B 675 MET cc_start: 0.5130 (mmp) cc_final: 0.4763 (mmp) REVERT: C 236 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7576 (tp) REVERT: C 242 MET cc_start: 0.7462 (tpp) cc_final: 0.7036 (tpp) REVERT: C 278 ASP cc_start: 0.8106 (m-30) cc_final: 0.7619 (m-30) REVERT: C 517 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7230 (mp) REVERT: C 522 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8045 (tt) REVERT: C 591 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6646 (m) REVERT: D 276 MET cc_start: 0.7643 (ppp) cc_final: 0.7319 (ptp) REVERT: D 295 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5284 (tmm) REVERT: D 344 CYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3601 (t) REVERT: D 471 PHE cc_start: 0.6782 (m-80) cc_final: 0.5354 (t80) REVERT: D 485 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6341 (t80) REVERT: D 593 CYS cc_start: 0.3015 (p) cc_final: 0.2632 (m) REVERT: D 608 PHE cc_start: 0.7514 (t80) cc_final: 0.7163 (t80) outliers start: 72 outliers final: 19 residues processed: 328 average time/residue: 0.2833 time to fit residues: 109.4044 Evaluate side-chains 251 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 151 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN C 674 ASN D 245 ASN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN D 613 GLN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.149959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.124672 restraints weight = 32648.018| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.90 r_work: 0.3755 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 1.1756 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= 0.141 Angle : 0.813 15.130 22044 Z= 0.371 Chirality : 0.043 0.187 2468 Planarity : 0.004 0.043 2708 Dihedral : 16.643 176.173 2400 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.07 % Allowed : 24.00 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 1856 helix: 1.03 (0.16), residues: 964 sheet: -0.80 (0.42), residues: 164 loop : -2.08 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 322 TYR 0.016 0.001 TYR A 227 PHE 0.025 0.002 PHE B 538 TRP 0.024 0.001 TRP D 280 HIS 0.002 0.000 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00295 (16196) covalent geometry : angle 0.78169 (22000) SS BOND : bond 0.00143 ( 4) SS BOND : angle 2.20290 ( 8) hydrogen bonds : bond 0.03909 ( 805) hydrogen bonds : angle 3.92386 ( 2463) link_NAG-ASN : bond 0.01066 ( 12) link_NAG-ASN : angle 5.47187 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3226 (tm) REVERT: A 242 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6112 (tpp) REVERT: A 583 MET cc_start: 0.5593 (ppp) cc_final: 0.5227 (ttt) REVERT: A 669 PHE cc_start: 0.7746 (m-80) cc_final: 0.7503 (m-10) REVERT: B 312 GLU cc_start: 0.7833 (pt0) cc_final: 0.7450 (pm20) REVERT: B 353 GLU cc_start: 0.9040 (tt0) cc_final: 0.8728 (tp30) REVERT: B 406 VAL cc_start: 0.8613 (t) cc_final: 0.8359 (m) REVERT: B 502 TYR cc_start: 0.6492 (t80) cc_final: 0.6165 (t80) REVERT: B 503 PHE cc_start: 0.5248 (p90) cc_final: 0.4969 (m-10) REVERT: B 595 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.5521 (tmtt) REVERT: B 611 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 669 PHE cc_start: 0.6175 (p90) cc_final: 0.5854 (m-10) REVERT: B 670 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6827 (t80) REVERT: B 675 MET cc_start: 0.5420 (mmp) cc_final: 0.5169 (mmp) REVERT: C 242 MET cc_start: 0.7655 (tpp) cc_final: 0.7330 (tpp) REVERT: C 267 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7472 (mmtm) REVERT: C 278 ASP cc_start: 0.8127 (m-30) cc_final: 0.7664 (m-30) REVERT: C 312 GLU cc_start: 0.8208 (pt0) cc_final: 0.7853 (pm20) REVERT: C 517 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6940 (mp) REVERT: C 660 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.5309 (t80) REVERT: D 292 TYR cc_start: 0.6785 (m-80) cc_final: 0.6556 (m-10) REVERT: D 324 LEU cc_start: 0.6764 (mt) cc_final: 0.6534 (mm) REVERT: D 344 CYS cc_start: 0.4301 (OUTLIER) cc_final: 0.3326 (t) REVERT: D 471 PHE cc_start: 0.6670 (m-80) cc_final: 0.5506 (t80) REVERT: D 485 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6748 (t80) REVERT: D 590 MET cc_start: 0.6910 (tpp) cc_final: 0.6443 (tpp) REVERT: D 593 CYS cc_start: 0.3181 (p) cc_final: 0.2656 (m) REVERT: D 637 PHE cc_start: 0.8701 (m-80) cc_final: 0.8023 (m-80) outliers start: 69 outliers final: 18 residues processed: 289 average time/residue: 0.2790 time to fit residues: 94.3634 Evaluate side-chains 227 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN C 559 ASN C 636 GLN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.120128 restraints weight = 32437.092| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.87 r_work: 0.3706 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 1.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16212 Z= 0.141 Angle : 0.790 13.910 22044 Z= 0.362 Chirality : 0.043 0.205 2468 Planarity : 0.004 0.042 2708 Dihedral : 16.545 176.493 2400 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.01 % Allowed : 25.88 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.19), residues: 1856 helix: 1.00 (0.16), residues: 964 sheet: -0.71 (0.42), residues: 176 loop : -2.05 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.020 0.001 TYR C 348 PHE 0.038 0.002 PHE B 483 TRP 0.022 0.001 TRP A 366 HIS 0.004 0.000 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00293 (16196) covalent geometry : angle 0.76340 (22000) SS BOND : bond 0.00871 ( 4) SS BOND : angle 2.09550 ( 8) hydrogen bonds : bond 0.03875 ( 805) hydrogen bonds : angle 3.94242 ( 2463) link_NAG-ASN : bond 0.01077 ( 12) link_NAG-ASN : angle 5.03445 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.3144 (tm) REVERT: A 293 TRP cc_start: 0.8063 (m100) cc_final: 0.7805 (m100) REVERT: A 583 MET cc_start: 0.5704 (ppp) cc_final: 0.5350 (ttt) REVERT: B 312 GLU cc_start: 0.8049 (pt0) cc_final: 0.7796 (pt0) REVERT: B 353 GLU cc_start: 0.9038 (tt0) cc_final: 0.8722 (tp30) REVERT: B 502 TYR cc_start: 0.6564 (t80) cc_final: 0.6192 (t80) REVERT: B 503 PHE cc_start: 0.5286 (p90) cc_final: 0.5019 (m-10) REVERT: B 595 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5711 (tmtt) REVERT: B 603 MET cc_start: 0.7896 (tmm) cc_final: 0.7123 (tpt) REVERT: B 611 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8139 (t80) REVERT: B 669 PHE cc_start: 0.6252 (p90) cc_final: 0.6024 (m-10) REVERT: B 670 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7018 (t80) REVERT: B 675 MET cc_start: 0.5613 (mmp) cc_final: 0.5380 (mmp) REVERT: C 236 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7689 (tp) REVERT: C 242 MET cc_start: 0.7806 (tpp) cc_final: 0.7265 (tpp) REVERT: C 267 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7622 (mmtm) REVERT: C 278 ASP cc_start: 0.8291 (m-30) cc_final: 0.7916 (m-30) REVERT: C 312 GLU cc_start: 0.8445 (pt0) cc_final: 0.7889 (pm20) REVERT: C 517 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6959 (mp) REVERT: C 637 PHE cc_start: 0.8847 (m-80) cc_final: 0.8116 (m-80) REVERT: C 648 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7539 (mt-10) REVERT: C 660 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6648 (t80) REVERT: C 675 MET cc_start: 0.6082 (mmm) cc_final: 0.5843 (mmp) REVERT: D 255 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8736 (tm-30) REVERT: D 278 ASP cc_start: 0.6902 (m-30) cc_final: 0.6491 (m-30) REVERT: D 321 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8061 (mm) REVERT: D 344 CYS cc_start: 0.3825 (OUTLIER) cc_final: 0.2774 (t) REVERT: D 471 PHE cc_start: 0.6908 (m-80) cc_final: 0.5758 (t80) REVERT: D 485 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6948 (t80) REVERT: D 567 PHE cc_start: 0.6830 (t80) cc_final: 0.6380 (t80) REVERT: D 590 MET cc_start: 0.7116 (tpp) cc_final: 0.6822 (tpp) REVERT: D 593 CYS cc_start: 0.3462 (p) cc_final: 0.2807 (m) REVERT: D 648 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7787 (mt-10) outliers start: 68 outliers final: 21 residues processed: 273 average time/residue: 0.3126 time to fit residues: 99.2331 Evaluate side-chains 225 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C 255 GLN C 613 GLN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.141424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115809 restraints weight = 32365.504| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.84 r_work: 0.3647 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 1.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16212 Z= 0.149 Angle : 0.811 13.235 22044 Z= 0.373 Chirality : 0.044 0.193 2468 Planarity : 0.004 0.041 2708 Dihedral : 16.524 176.410 2400 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.42 % Allowed : 27.24 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.19), residues: 1856 helix: 1.02 (0.17), residues: 944 sheet: -0.73 (0.41), residues: 176 loop : -2.04 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 251 TYR 0.046 0.001 TYR A 611 PHE 0.046 0.002 PHE B 485 TRP 0.022 0.001 TRP A 366 HIS 0.001 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00329 (16196) covalent geometry : angle 0.78767 (22000) SS BOND : bond 0.00233 ( 4) SS BOND : angle 2.25955 ( 8) hydrogen bonds : bond 0.03940 ( 805) hydrogen bonds : angle 3.95432 ( 2463) link_NAG-ASN : bond 0.00908 ( 12) link_NAG-ASN : angle 4.72549 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.3619 (OUTLIER) cc_final: 0.3347 (tm) REVERT: A 293 TRP cc_start: 0.8347 (m100) cc_final: 0.7806 (m100) REVERT: A 583 MET cc_start: 0.5493 (ppp) cc_final: 0.5256 (ttt) REVERT: B 242 MET cc_start: 0.8100 (tpp) cc_final: 0.7721 (tpp) REVERT: B 312 GLU cc_start: 0.8114 (pt0) cc_final: 0.7585 (pm20) REVERT: B 353 GLU cc_start: 0.9090 (tt0) cc_final: 0.8743 (tp30) REVERT: B 502 TYR cc_start: 0.6860 (t80) cc_final: 0.6469 (t80) REVERT: B 503 PHE cc_start: 0.5401 (p90) cc_final: 0.5066 (m-10) REVERT: B 611 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8100 (t80) REVERT: B 650 GLU cc_start: 0.8311 (tt0) cc_final: 0.7717 (tp30) REVERT: B 669 PHE cc_start: 0.6178 (p90) cc_final: 0.5969 (m-10) REVERT: B 670 PHE cc_start: 0.7433 (t80) cc_final: 0.7094 (t80) REVERT: B 675 MET cc_start: 0.5621 (mmp) cc_final: 0.5358 (mmp) REVERT: C 236 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7677 (tp) REVERT: C 242 MET cc_start: 0.7750 (tpp) cc_final: 0.7432 (tpp) REVERT: C 267 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7859 (mppt) REVERT: C 278 ASP cc_start: 0.8421 (m-30) cc_final: 0.8116 (m-30) REVERT: C 517 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7017 (mp) REVERT: C 529 THR cc_start: 0.8199 (t) cc_final: 0.7993 (p) REVERT: C 591 SER cc_start: 0.6215 (OUTLIER) cc_final: 0.5891 (m) REVERT: C 637 PHE cc_start: 0.8865 (m-80) cc_final: 0.8663 (m-80) REVERT: C 648 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7745 (mt-10) REVERT: C 660 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6730 (t80) REVERT: C 675 MET cc_start: 0.6270 (mmm) cc_final: 0.5956 (mmp) REVERT: D 252 MET cc_start: 0.8133 (tmm) cc_final: 0.7705 (tpp) REVERT: D 255 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8766 (tm-30) REVERT: D 278 ASP cc_start: 0.7400 (m-30) cc_final: 0.6899 (m-30) REVERT: D 295 MET cc_start: 0.7222 (ttm) cc_final: 0.6710 (tmm) REVERT: D 310 PHE cc_start: 0.8631 (m-80) cc_final: 0.8419 (m-80) REVERT: D 471 PHE cc_start: 0.6877 (m-80) cc_final: 0.5701 (t80) REVERT: D 590 MET cc_start: 0.7346 (tpp) cc_final: 0.7076 (tpp) REVERT: D 593 CYS cc_start: 0.3698 (p) cc_final: 0.2984 (m) REVERT: D 648 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7918 (mt-10) outliers start: 58 outliers final: 21 residues processed: 268 average time/residue: 0.3068 time to fit residues: 96.2348 Evaluate side-chains 227 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 313 ASN C 555 GLN C 559 ASN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105541 restraints weight = 32382.070| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.72 r_work: 0.3510 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 1.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16212 Z= 0.181 Angle : 0.857 12.549 22044 Z= 0.405 Chirality : 0.046 0.287 2468 Planarity : 0.004 0.059 2708 Dihedral : 16.704 176.177 2400 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.18 % Allowed : 28.77 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.19), residues: 1856 helix: 0.83 (0.16), residues: 968 sheet: -0.54 (0.42), residues: 168 loop : -2.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 251 TYR 0.024 0.002 TYR B 348 PHE 0.022 0.002 PHE C 605 TRP 0.027 0.002 TRP A 366 HIS 0.002 0.000 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00386 (16196) covalent geometry : angle 0.83388 (22000) SS BOND : bond 0.01239 ( 4) SS BOND : angle 3.82536 ( 8) hydrogen bonds : bond 0.04631 ( 805) hydrogen bonds : angle 4.12185 ( 2463) link_NAG-ASN : bond 0.00855 ( 12) link_NAG-ASN : angle 4.68849 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8644 (m-30) cc_final: 0.8246 (m-30) REVERT: A 342 LYS cc_start: 0.8839 (mppt) cc_final: 0.8201 (mmtt) REVERT: A 477 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7346 (tt0) REVERT: A 602 ILE cc_start: 0.8151 (pt) cc_final: 0.7888 (pp) REVERT: A 605 PHE cc_start: 0.8276 (t80) cc_final: 0.7966 (t80) REVERT: B 242 MET cc_start: 0.8398 (tpp) cc_final: 0.8140 (tpp) REVERT: B 278 ASP cc_start: 0.8205 (m-30) cc_final: 0.7828 (m-30) REVERT: B 295 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5298 (mtp) REVERT: B 312 GLU cc_start: 0.8428 (pt0) cc_final: 0.7630 (pm20) REVERT: B 502 TYR cc_start: 0.7011 (t80) cc_final: 0.6716 (t80) REVERT: B 503 PHE cc_start: 0.5988 (p90) cc_final: 0.5300 (m-10) REVERT: B 611 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 669 PHE cc_start: 0.6436 (p90) cc_final: 0.6057 (m-10) REVERT: B 670 PHE cc_start: 0.7573 (t80) cc_final: 0.7286 (t80) REVERT: B 675 MET cc_start: 0.5810 (mmp) cc_final: 0.5589 (mmp) REVERT: C 236 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7833 (tp) REVERT: C 242 MET cc_start: 0.8312 (tpp) cc_final: 0.7842 (tpp) REVERT: C 267 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8171 (mmtm) REVERT: C 278 ASP cc_start: 0.8626 (m-30) cc_final: 0.8346 (m-30) REVERT: C 312 GLU cc_start: 0.8519 (pt0) cc_final: 0.7862 (pm20) REVERT: C 611 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8045 (t80) REVERT: C 613 GLN cc_start: 0.7545 (tp40) cc_final: 0.7345 (tm-30) REVERT: C 617 LEU cc_start: 0.8328 (tm) cc_final: 0.8102 (tp) REVERT: C 648 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8066 (mt-10) REVERT: D 252 MET cc_start: 0.8463 (tmm) cc_final: 0.7975 (tpp) REVERT: D 253 MET cc_start: 0.9149 (tpp) cc_final: 0.8725 (mmm) REVERT: D 255 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: D 277 GLU cc_start: 0.8558 (tp30) cc_final: 0.8358 (tp30) REVERT: D 278 ASP cc_start: 0.8183 (m-30) cc_final: 0.7824 (m-30) REVERT: D 295 MET cc_start: 0.7489 (ttm) cc_final: 0.7115 (tpp) REVERT: D 593 CYS cc_start: 0.4296 (p) cc_final: 0.3500 (m) REVERT: D 650 GLU cc_start: 0.8449 (pp20) cc_final: 0.8112 (tt0) outliers start: 54 outliers final: 18 residues processed: 274 average time/residue: 0.3128 time to fit residues: 99.7512 Evaluate side-chains 213 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 607 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN C 255 GLN D 245 ASN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106174 restraints weight = 32447.545| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.77 r_work: 0.3518 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 1.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16212 Z= 0.146 Angle : 0.852 14.735 22044 Z= 0.390 Chirality : 0.044 0.256 2468 Planarity : 0.004 0.061 2708 Dihedral : 16.641 177.710 2400 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.36 % Allowed : 31.19 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.19), residues: 1856 helix: 0.83 (0.16), residues: 968 sheet: -0.56 (0.42), residues: 168 loop : -2.08 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 251 TYR 0.032 0.002 TYR B 348 PHE 0.024 0.002 PHE C 605 TRP 0.021 0.001 TRP A 366 HIS 0.001 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00318 (16196) covalent geometry : angle 0.83304 (22000) SS BOND : bond 0.00213 ( 4) SS BOND : angle 2.75513 ( 8) hydrogen bonds : bond 0.04022 ( 805) hydrogen bonds : angle 4.01500 ( 2463) link_NAG-ASN : bond 0.00833 ( 12) link_NAG-ASN : angle 4.34613 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.590 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: 0.8556 (m-30) cc_final: 0.8183 (m-30) REVERT: A 293 TRP cc_start: 0.8325 (m100) cc_final: 0.8102 (m100) REVERT: A 342 LYS cc_start: 0.8835 (mppt) cc_final: 0.8224 (mmtt) REVERT: A 477 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7565 (tt0) REVERT: B 242 MET cc_start: 0.8292 (tpp) cc_final: 0.8005 (tpp) REVERT: B 278 ASP cc_start: 0.8186 (m-30) cc_final: 0.7853 (m-30) REVERT: B 295 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5027 (ttp) REVERT: B 502 TYR cc_start: 0.7171 (t80) cc_final: 0.6919 (t80) REVERT: B 503 PHE cc_start: 0.5954 (p90) cc_final: 0.5359 (m-10) REVERT: B 611 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 669 PHE cc_start: 0.6323 (p90) cc_final: 0.5879 (m-10) REVERT: B 670 PHE cc_start: 0.7574 (t80) cc_final: 0.7291 (t80) REVERT: C 236 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 242 MET cc_start: 0.8242 (tpp) cc_final: 0.7907 (tpp) REVERT: C 267 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8196 (mmtm) REVERT: C 278 ASP cc_start: 0.8580 (m-30) cc_final: 0.8303 (m-30) REVERT: C 613 GLN cc_start: 0.7673 (tp40) cc_final: 0.7460 (tm-30) REVERT: C 617 LEU cc_start: 0.8253 (tm) cc_final: 0.7979 (tp) REVERT: C 648 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8259 (mt-10) REVERT: C 669 PHE cc_start: 0.6937 (m-10) cc_final: 0.6645 (t80) REVERT: D 252 MET cc_start: 0.8476 (tmm) cc_final: 0.8062 (tpp) REVERT: D 253 MET cc_start: 0.9120 (tpp) cc_final: 0.8668 (mmm) REVERT: D 278 ASP cc_start: 0.8063 (m-30) cc_final: 0.7784 (m-30) REVERT: D 295 MET cc_start: 0.7454 (ttm) cc_final: 0.7159 (tpp) REVERT: D 506 PHE cc_start: 0.6833 (t80) cc_final: 0.5935 (p90) REVERT: D 593 CYS cc_start: 0.3776 (p) cc_final: 0.3178 (m) REVERT: D 650 GLU cc_start: 0.8329 (pp20) cc_final: 0.8102 (tt0) outliers start: 40 outliers final: 17 residues processed: 240 average time/residue: 0.3090 time to fit residues: 86.8065 Evaluate side-chains 211 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 456 GLN B 613 GLN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095053 restraints weight = 32755.663| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.57 r_work: 0.3355 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 1.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16212 Z= 0.238 Angle : 0.982 13.759 22044 Z= 0.470 Chirality : 0.050 0.275 2468 Planarity : 0.005 0.058 2708 Dihedral : 17.158 179.422 2400 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.77 % Allowed : 32.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.19), residues: 1856 helix: 0.52 (0.16), residues: 960 sheet: -1.07 (0.41), residues: 176 loop : -2.26 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 251 TYR 0.038 0.003 TYR A 502 PHE 0.031 0.003 PHE A 426 TRP 0.031 0.002 TRP D 414 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00555 (16196) covalent geometry : angle 0.96171 (22000) SS BOND : bond 0.00229 ( 4) SS BOND : angle 3.63458 ( 8) hydrogen bonds : bond 0.05605 ( 805) hydrogen bonds : angle 4.40936 ( 2463) link_NAG-ASN : bond 0.00832 ( 12) link_NAG-ASN : angle 4.75127 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8723 (m-30) cc_final: 0.8350 (m-30) REVERT: A 293 TRP cc_start: 0.8756 (m100) cc_final: 0.8451 (m100) REVERT: A 342 LYS cc_start: 0.8932 (mppt) cc_final: 0.8498 (mmtt) REVERT: A 477 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7913 (tt0) REVERT: A 605 PHE cc_start: 0.8310 (t80) cc_final: 0.8006 (t80) REVERT: A 675 MET cc_start: 0.6948 (ppp) cc_final: 0.6645 (tpt) REVERT: A 681 ASN cc_start: 0.8768 (m-40) cc_final: 0.8286 (p0) REVERT: B 278 ASP cc_start: 0.8316 (m-30) cc_final: 0.7899 (t0) REVERT: B 295 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5724 (ttp) REVERT: B 312 GLU cc_start: 0.8399 (pt0) cc_final: 0.7831 (pm20) REVERT: B 577 ILE cc_start: 0.5386 (OUTLIER) cc_final: 0.5083 (tp) REVERT: B 611 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7946 (t80) REVERT: B 669 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6449 (m-10) REVERT: C 236 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 242 MET cc_start: 0.8446 (tpp) cc_final: 0.8170 (tpp) REVERT: C 278 ASP cc_start: 0.8596 (m-30) cc_final: 0.8281 (m-30) REVERT: C 502 TYR cc_start: 0.6291 (t80) cc_final: 0.5010 (t80) REVERT: C 531 ASN cc_start: 0.8227 (t0) cc_final: 0.6839 (m110) REVERT: C 583 MET cc_start: 0.0799 (mmp) cc_final: 0.0306 (mmm) REVERT: C 669 PHE cc_start: 0.7074 (m-10) cc_final: 0.6837 (t80) REVERT: C 675 MET cc_start: 0.6428 (mmp) cc_final: 0.5983 (mmt) REVERT: D 252 MET cc_start: 0.8436 (tmm) cc_final: 0.8080 (tpp) REVERT: D 253 MET cc_start: 0.9189 (tpp) cc_final: 0.8764 (mmm) REVERT: D 255 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: D 278 ASP cc_start: 0.8416 (m-30) cc_final: 0.7936 (m-30) REVERT: D 593 CYS cc_start: 0.3847 (p) cc_final: 0.3420 (m) REVERT: D 669 PHE cc_start: 0.7059 (m-10) cc_final: 0.6059 (t80) REVERT: D 670 PHE cc_start: 0.7500 (t80) cc_final: 0.7167 (t80) REVERT: D 673 LEU cc_start: 0.8270 (mp) cc_final: 0.7699 (mp) outliers start: 30 outliers final: 12 residues processed: 228 average time/residue: 0.3264 time to fit residues: 86.4605 Evaluate side-chains 187 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 264 LYS 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 25 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098458 restraints weight = 32606.958| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.60 r_work: 0.3411 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 1.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16212 Z= 0.161 Angle : 0.908 15.497 22044 Z= 0.421 Chirality : 0.045 0.253 2468 Planarity : 0.004 0.050 2708 Dihedral : 16.952 179.725 2400 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.71 % Allowed : 33.67 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.19), residues: 1856 helix: 0.94 (0.16), residues: 952 sheet: -0.37 (0.44), residues: 156 loop : -2.36 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 251 TYR 0.030 0.002 TYR C 348 PHE 0.032 0.002 PHE B 485 TRP 0.022 0.001 TRP D 414 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00358 (16196) covalent geometry : angle 0.88856 (22000) SS BOND : bond 0.00310 ( 4) SS BOND : angle 3.57363 ( 8) hydrogen bonds : bond 0.04466 ( 805) hydrogen bonds : angle 4.12543 ( 2463) link_NAG-ASN : bond 0.00862 ( 12) link_NAG-ASN : angle 4.46142 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3367.24 seconds wall clock time: 58 minutes 17.17 seconds (3497.17 seconds total)