Starting phenix.real_space_refine on Sun Apr 5 19:54:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x57_66576/04_2026/9x57_66576.map" } resolution = 3.5 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8266 2.51 5 N 2066 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12734 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3179 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain breaks: 1 Chain: "C" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3179 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASP A 592 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 592 " occ=0.60 residue: pdb=" N ASP C 592 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP C 592 " occ=0.60 Time building chain proxies: 3.00, per 1000 atoms: 0.24 Number of scatterers: 12734 At special positions: 0 Unit cell: (122.1, 124.3, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2322 8.00 N 2066 7.00 C 8266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 775 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 775 " distance=2.03 Simple disulfide: pdb=" SG CYS D 720 " - pdb=" SG CYS D 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 775 " 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 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 709.2 milliseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 18 sheets defined 49.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.676A pdb=" N LYS A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.709A pdb=" N LEU A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.568A pdb=" N TRP A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 548 Processing helix chain 'A' and resid 577 through 585 removed outlier: 3.738A pdb=" N SER A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.550A pdb=" N GLY A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 609 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.829A pdb=" N GLN A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 666 through 678 removed outlier: 4.089A pdb=" N SER A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.683A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 716 removed outlier: 3.782A pdb=" N TYR A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.719A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 770 removed outlier: 4.017A pdb=" N LYS A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 820 removed outlier: 3.528A pdb=" N TYR A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 removed outlier: 3.602A pdb=" N ASP B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.703A pdb=" N TYR B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 524 through 549 Processing helix chain 'B' and resid 575 through 587 Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.685A pdb=" N ALA B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.993A pdb=" N ALA B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 Processing helix chain 'B' and resid 666 through 679 removed outlier: 3.745A pdb=" N SER B 678 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 698 removed outlier: 3.537A pdb=" N ARG B 696 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 744 through 759 Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'B' and resid 790 through 793 Processing helix chain 'B' and resid 794 through 823 removed outlier: 4.050A pdb=" N PHE B 798 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 439 removed outlier: 3.547A pdb=" N ASP D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.760A pdb=" N LEU D 469 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 524 through 549 removed outlier: 3.508A pdb=" N TRP D 528 " --> pdb=" O ALA D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 Processing helix chain 'D' and resid 600 through 626 removed outlier: 3.690A pdb=" N ALA D 624 " --> pdb=" O ALA D 620 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.714A pdb=" N ALA D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 663 Processing helix chain 'D' and resid 666 through 679 removed outlier: 3.566A pdb=" N MET D 672 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 698 Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.552A pdb=" N GLN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 759 removed outlier: 3.657A pdb=" N GLY D 759 " --> pdb=" O LEU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 770 removed outlier: 4.126A pdb=" N LYS D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 823 removed outlier: 4.060A pdb=" N PHE D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 425 through 439 Processing helix chain 'C' and resid 457 through 460 removed outlier: 3.676A pdb=" N LYS C 460 " --> pdb=" O ALA C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 465 through 472 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 517 through 521 removed outlier: 3.709A pdb=" N LEU C 520 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.569A pdb=" N TRP C 528 " --> pdb=" O ALA C 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 532 " --> pdb=" O TRP C 528 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 533 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 577 through 585 removed outlier: 3.738A pdb=" N SER C 582 " --> pdb=" O SER C 578 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.550A pdb=" N GLY C 605 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 613 " --> pdb=" O PHE C 609 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 623 " --> pdb=" O THR C 619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 644 removed outlier: 3.829A pdb=" N GLN C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'C' and resid 666 through 678 removed outlier: 4.089A pdb=" N SER C 678 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.682A pdb=" N SER C 698 " --> pdb=" O ARG C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 716 removed outlier: 3.782A pdb=" N TYR C 713 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 759 removed outlier: 3.719A pdb=" N LEU C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 770 removed outlier: 4.017A pdb=" N LYS C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 820 removed outlier: 3.528A pdb=" N TYR C 799 " --> pdb=" O ALA C 795 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.439A pdb=" N VAL A 397 " --> pdb=" O LYS A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.628A pdb=" N MET A 409 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 424 " --> pdb=" O MET A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AA4, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.767A pdb=" N ILE A 504 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 442 through 446 removed outlier: 6.022A pdb=" N VAL B 397 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 445 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL B 399 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 476 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AA7, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA8, first strand: chain 'B' and resid 499 through 500 Processing sheet with id=AA9, first strand: chain 'B' and resid 648 through 650 removed outlier: 6.902A pdb=" N ALA B 648 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU B 705 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY B 650 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N GLU B 707 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N PHE B 702 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 507 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 504 " --> pdb=" O VAL B 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.113A pdb=" N VAL D 397 " --> pdb=" O LYS D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AB3, first strand: chain 'D' and resid 491 through 492 Processing sheet with id=AB4, first strand: chain 'D' and resid 498 through 500 removed outlier: 4.111A pdb=" N MET D 498 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 732 " --> pdb=" O LEU D 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 648 through 650 removed outlier: 6.926A pdb=" N ALA D 648 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU D 705 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY D 650 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLU D 707 " --> pdb=" O GLY D 650 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N PHE D 702 " --> pdb=" O LYS D 507 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS D 507 " --> pdb=" O PHE D 702 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 504 " --> pdb=" O VAL D 725 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.440A pdb=" N VAL C 397 " --> pdb=" O LYS C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 409 through 410 removed outlier: 3.627A pdb=" N MET C 409 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 424 " --> pdb=" O MET C 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AB9, first strand: chain 'C' and resid 504 through 507 removed outlier: 3.767A pdb=" N ILE C 504 " --> pdb=" O VAL C 725 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1503 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: 1.89 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3908 1.34 - 1.46: 3159 1.46 - 1.58: 5815 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 13018 Sorted by residual: bond pdb=" CA GLY B 655 " pdb=" C GLY B 655 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.93e+00 bond pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta sigma weight residual 1.464 1.450 0.015 1.12e-02 7.97e+03 1.72e+00 bond pdb=" CA ASN C 413 " pdb=" CB ASN C 413 " ideal model delta sigma weight residual 1.527 1.549 -0.021 1.70e-02 3.46e+03 1.59e+00 bond pdb=" CA ASN A 413 " pdb=" CB ASN A 413 " ideal model delta sigma weight residual 1.527 1.548 -0.021 1.70e-02 3.46e+03 1.49e+00 bond pdb=" C ASP A 521 " pdb=" N PRO A 522 " ideal model delta sigma weight residual 1.334 1.362 -0.029 2.34e-02 1.83e+03 1.48e+00 ... (remaining 13013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17323 2.14 - 4.28: 213 4.28 - 6.42: 27 6.42 - 8.56: 3 8.56 - 10.69: 2 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N VAL C 628 " pdb=" CA VAL C 628 " pdb=" C VAL C 628 " ideal model delta sigma weight residual 112.98 108.98 4.00 1.25e+00 6.40e-01 1.03e+01 angle pdb=" N VAL A 628 " pdb=" CA VAL A 628 " pdb=" C VAL A 628 " ideal model delta sigma weight residual 112.98 108.98 4.00 1.25e+00 6.40e-01 1.02e+01 angle pdb=" N MET B 403 " pdb=" CA MET B 403 " pdb=" C MET B 403 " ideal model delta sigma weight residual 109.31 113.78 -4.47 1.42e+00 4.96e-01 9.90e+00 angle pdb=" CA LEU C 641 " pdb=" CB LEU C 641 " pdb=" CG LEU C 641 " ideal model delta sigma weight residual 116.30 126.99 -10.69 3.50e+00 8.16e-02 9.34e+00 angle pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " pdb=" CG LEU A 641 " ideal model delta sigma weight residual 116.30 126.97 -10.67 3.50e+00 8.16e-02 9.30e+00 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6563 17.66 - 35.32: 919 35.32 - 52.98: 221 52.98 - 70.63: 36 70.63 - 88.29: 21 Dihedral angle restraints: 7760 sinusoidal: 3078 harmonic: 4682 Sorted by residual: dihedral pdb=" CA THR C 645 " pdb=" C THR C 645 " pdb=" N GLU C 646 " pdb=" CA GLU C 646 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR A 645 " pdb=" C THR A 645 " pdb=" N GLU A 646 " pdb=" CA GLU A 646 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLY B 472 " pdb=" C GLY B 472 " pdb=" N LYS B 473 " pdb=" CA LYS B 473 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1350 0.037 - 0.073: 436 0.073 - 0.110: 139 0.110 - 0.146: 29 0.146 - 0.183: 4 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CB VAL C 545 " pdb=" CA VAL C 545 " pdb=" CG1 VAL C 545 " pdb=" CG2 VAL C 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CB VAL A 545 " pdb=" CA VAL A 545 " pdb=" CG1 VAL A 545 " pdb=" CG2 VAL A 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ASN A 413 " pdb=" N ASN A 413 " pdb=" C ASN A 413 " pdb=" CB ASN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 1955 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 420 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN D 420 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 420 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 421 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 447 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 448 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 447 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO C 448 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 448 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 448 " -0.028 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2662 2.77 - 3.31: 11646 3.31 - 3.84: 19391 3.84 - 4.37: 20493 4.37 - 4.90: 37890 Nonbonded interactions: 92082 Sorted by model distance: nonbonded pdb=" OD2 ASP D 456 " pdb=" OG1 THR D 459 " model vdw 2.242 3.040 nonbonded pdb=" N GLU B 415 " pdb=" OE1 GLU B 415 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP C 730 " pdb=" NZ LYS C 732 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP A 730 " pdb=" NZ LYS A 732 " model vdw 2.295 3.120 nonbonded pdb=" O ASP A 458 " pdb=" OG1 THR A 459 " model vdw 2.301 3.040 ... (remaining 92077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 550 or resid 572 through 821)) selection = (chain 'B' and resid 395 through 821) selection = (chain 'C' and (resid 395 through 550 or resid 572 through 821)) selection = (chain 'D' and resid 395 through 821) } 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 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: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.440 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.003 0.032 13022 Z= 0.137 Angle : 0.594 10.695 17576 Z= 0.323 Chirality : 0.041 0.183 1958 Planarity : 0.004 0.050 2172 Dihedral : 17.172 88.292 4760 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 29.11 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1614 helix: 0.32 (0.20), residues: 766 sheet: -1.64 (0.41), residues: 160 loop : -2.85 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 677 TYR 0.021 0.001 TYR B 818 PHE 0.014 0.001 PHE D 417 TRP 0.012 0.001 TRP A 580 HIS 0.005 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00305 (13018) covalent geometry : angle 0.59397 (17568) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.28443 ( 8) hydrogen bonds : bond 0.17853 ( 509) hydrogen bonds : angle 6.16516 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 415 GLU cc_start: 0.6510 (pm20) cc_final: 0.6181 (mp0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1203 time to fit residues: 25.1282 Evaluate side-chains 132 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 414 HIS ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141150 restraints weight = 17114.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140880 restraints weight = 27792.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141679 restraints weight = 27154.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143010 restraints weight = 16169.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143485 restraints weight = 13462.575| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13022 Z= 0.122 Angle : 0.533 6.925 17576 Z= 0.281 Chirality : 0.041 0.151 1958 Planarity : 0.003 0.044 2172 Dihedral : 3.927 20.695 1758 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.98 % Allowed : 26.78 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1614 helix: 0.82 (0.20), residues: 792 sheet: -1.41 (0.42), residues: 154 loop : -2.79 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 677 TYR 0.014 0.001 TYR D 818 PHE 0.013 0.001 PHE B 497 TRP 0.009 0.001 TRP A 607 HIS 0.003 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00286 (13018) covalent geometry : angle 0.53313 (17568) SS BOND : bond 0.00885 ( 4) SS BOND : angle 0.66141 ( 8) hydrogen bonds : bond 0.04748 ( 509) hydrogen bonds : angle 4.30508 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7502 (tp30) REVERT: D 762 ASP cc_start: 0.7890 (p0) cc_final: 0.7521 (p0) REVERT: C 815 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7525 (tp30) outliers start: 41 outliers final: 21 residues processed: 175 average time/residue: 0.1064 time to fit residues: 27.2410 Evaluate side-chains 150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 765 LYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 76 optimal weight: 0.4980 chunk 12 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 414 HIS D 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139631 restraints weight = 16952.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140030 restraints weight = 22978.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140667 restraints weight = 25360.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141357 restraints weight = 14666.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142297 restraints weight = 12375.698| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13022 Z= 0.111 Angle : 0.512 6.720 17576 Z= 0.269 Chirality : 0.040 0.159 1958 Planarity : 0.003 0.043 2172 Dihedral : 3.798 19.696 1758 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.64 % Allowed : 26.93 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1614 helix: 1.08 (0.20), residues: 796 sheet: -1.30 (0.43), residues: 154 loop : -2.75 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.019 0.001 TYR B 818 PHE 0.012 0.001 PHE B 497 TRP 0.009 0.001 TRP C 580 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00261 (13018) covalent geometry : angle 0.51188 (17568) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.57945 ( 8) hydrogen bonds : bond 0.04111 ( 509) hydrogen bonds : angle 4.03753 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.480 Fit side-chains REVERT: A 815 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7403 (tp30) REVERT: B 452 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4643 (m-10) REVERT: D 762 ASP cc_start: 0.7979 (p0) cc_final: 0.7568 (p0) REVERT: D 809 MET cc_start: 0.7529 (mtp) cc_final: 0.7314 (mmm) REVERT: C 815 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7430 (tp30) outliers start: 50 outliers final: 22 residues processed: 177 average time/residue: 0.1114 time to fit residues: 29.1424 Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 711 ASN B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137109 restraints weight = 17031.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136803 restraints weight = 25315.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137485 restraints weight = 29874.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138921 restraints weight = 15641.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139622 restraints weight = 12512.348| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13022 Z= 0.150 Angle : 0.545 7.020 17576 Z= 0.287 Chirality : 0.041 0.156 1958 Planarity : 0.004 0.040 2172 Dihedral : 3.969 19.434 1758 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.22 % Allowed : 27.44 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.22), residues: 1614 helix: 1.03 (0.20), residues: 800 sheet: -2.04 (0.39), residues: 174 loop : -2.85 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 677 TYR 0.021 0.001 TYR B 818 PHE 0.018 0.001 PHE A 497 TRP 0.012 0.001 TRP C 580 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00371 (13018) covalent geometry : angle 0.54483 (17568) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.43699 ( 8) hydrogen bonds : bond 0.05093 ( 509) hydrogen bonds : angle 4.09993 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7227 (mtt) cc_final: 0.6978 (mtt) REVERT: A 815 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7326 (tp30) REVERT: B 452 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4949 (m-10) REVERT: D 767 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: C 465 MET cc_start: 0.7202 (mtt) cc_final: 0.6975 (mtt) REVERT: C 815 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7348 (tp30) outliers start: 58 outliers final: 39 residues processed: 174 average time/residue: 0.1141 time to fit residues: 28.9800 Evaluate side-chains 166 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 153 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138670 restraints weight = 17160.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139196 restraints weight = 27665.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139977 restraints weight = 22806.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142283 restraints weight = 14694.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142474 restraints weight = 10616.155| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13022 Z= 0.143 Angle : 0.538 6.868 17576 Z= 0.283 Chirality : 0.041 0.164 1958 Planarity : 0.003 0.040 2172 Dihedral : 3.951 19.043 1758 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.64 % Allowed : 28.02 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1614 helix: 1.07 (0.20), residues: 800 sheet: -2.04 (0.39), residues: 174 loop : -2.84 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.022 0.001 TYR B 818 PHE 0.016 0.001 PHE C 497 TRP 0.012 0.001 TRP C 580 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00352 (13018) covalent geometry : angle 0.53833 (17568) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.32734 ( 8) hydrogen bonds : bond 0.04843 ( 509) hydrogen bonds : angle 4.05584 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 465 MET cc_start: 0.7244 (mtt) cc_final: 0.7013 (mtt) REVERT: A 815 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7218 (tp30) REVERT: B 452 TYR cc_start: 0.5367 (OUTLIER) cc_final: 0.4934 (m-10) REVERT: D 767 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7640 (tttm) REVERT: C 465 MET cc_start: 0.7219 (mtt) cc_final: 0.7014 (mtt) REVERT: C 815 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7244 (tp30) outliers start: 50 outliers final: 39 residues processed: 164 average time/residue: 0.1110 time to fit residues: 26.6131 Evaluate side-chains 164 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133614 restraints weight = 17055.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131375 restraints weight = 24809.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132508 restraints weight = 27425.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135246 restraints weight = 17470.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136098 restraints weight = 12154.674| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13022 Z= 0.174 Angle : 0.561 7.237 17576 Z= 0.295 Chirality : 0.042 0.166 1958 Planarity : 0.004 0.039 2172 Dihedral : 4.076 18.939 1758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.02 % Allowed : 26.78 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1614 helix: 1.04 (0.20), residues: 798 sheet: -2.14 (0.39), residues: 174 loop : -2.86 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.023 0.002 TYR B 818 PHE 0.019 0.001 PHE C 497 TRP 0.013 0.001 TRP C 580 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00435 (13018) covalent geometry : angle 0.56129 (17568) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.34808 ( 8) hydrogen bonds : bond 0.05330 ( 509) hydrogen bonds : angle 4.12427 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 119 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 807 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 815 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7383 (tp30) REVERT: B 452 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.5123 (m-10) REVERT: D 767 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7830 (tttm) REVERT: C 807 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8314 (tt) REVERT: C 815 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7383 (tp30) outliers start: 69 outliers final: 41 residues processed: 179 average time/residue: 0.0993 time to fit residues: 26.8038 Evaluate side-chains 166 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 chunk 82 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 414 HIS D 414 HIS C 463 ASN C 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140650 restraints weight = 16813.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133290 restraints weight = 24141.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132035 restraints weight = 19003.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132087 restraints weight = 19851.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132185 restraints weight = 18026.452| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13022 Z= 0.130 Angle : 0.544 7.527 17576 Z= 0.286 Chirality : 0.041 0.166 1958 Planarity : 0.003 0.037 2172 Dihedral : 3.921 17.217 1758 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.22 % Allowed : 27.29 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1614 helix: 1.20 (0.20), residues: 796 sheet: -1.75 (0.44), residues: 146 loop : -2.81 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.024 0.001 TYR B 818 PHE 0.020 0.001 PHE B 417 TRP 0.011 0.001 TRP C 580 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00317 (13018) covalent geometry : angle 0.54406 (17568) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.29315 ( 8) hydrogen bonds : bond 0.04491 ( 509) hydrogen bonds : angle 3.96043 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 807 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 815 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7415 (tp30) REVERT: B 415 GLU cc_start: 0.6969 (pm20) cc_final: 0.6587 (mp0) REVERT: B 452 TYR cc_start: 0.5544 (OUTLIER) cc_final: 0.5092 (m-10) REVERT: D 417 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5405 (p90) REVERT: D 767 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7757 (tttm) REVERT: C 704 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8127 (t80) REVERT: C 807 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8259 (tt) REVERT: C 815 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7393 (tp30) outliers start: 58 outliers final: 42 residues processed: 178 average time/residue: 0.1070 time to fit residues: 28.3328 Evaluate side-chains 175 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 150 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.0020 chunk 16 optimal weight: 0.3980 overall best weight: 0.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140273 restraints weight = 16794.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134201 restraints weight = 24256.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132307 restraints weight = 18548.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132174 restraints weight = 20445.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132241 restraints weight = 19046.959| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13022 Z= 0.127 Angle : 0.544 8.838 17576 Z= 0.285 Chirality : 0.041 0.164 1958 Planarity : 0.003 0.038 2172 Dihedral : 3.872 17.305 1758 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.44 % Allowed : 27.22 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1614 helix: 1.27 (0.20), residues: 794 sheet: -1.71 (0.44), residues: 146 loop : -2.79 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 677 TYR 0.024 0.001 TYR B 818 PHE 0.014 0.001 PHE C 497 TRP 0.011 0.001 TRP C 580 HIS 0.004 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00309 (13018) covalent geometry : angle 0.54408 (17568) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.29834 ( 8) hydrogen bonds : bond 0.04393 ( 509) hydrogen bonds : angle 3.94027 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8121 (t80) REVERT: A 807 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 815 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7629 (tp30) REVERT: B 415 GLU cc_start: 0.6969 (pm20) cc_final: 0.6759 (mp0) REVERT: B 452 TYR cc_start: 0.5523 (OUTLIER) cc_final: 0.5154 (m-10) REVERT: D 767 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7800 (tttm) REVERT: C 704 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8126 (t80) REVERT: C 807 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 815 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7617 (tp30) outliers start: 61 outliers final: 49 residues processed: 176 average time/residue: 0.1079 time to fit residues: 28.4099 Evaluate side-chains 180 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 130 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140399 restraints weight = 16882.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139710 restraints weight = 27196.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140977 restraints weight = 22292.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142621 restraints weight = 15628.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143062 restraints weight = 13738.607| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13022 Z= 0.146 Angle : 0.562 9.891 17576 Z= 0.293 Chirality : 0.041 0.165 1958 Planarity : 0.003 0.037 2172 Dihedral : 3.928 17.358 1758 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.37 % Allowed : 27.15 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1614 helix: 1.22 (0.20), residues: 794 sheet: -2.07 (0.39), residues: 174 loop : -2.84 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 677 TYR 0.025 0.001 TYR B 818 PHE 0.016 0.001 PHE C 497 TRP 0.012 0.001 TRP C 580 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00362 (13018) covalent geometry : angle 0.56182 (17568) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.27037 ( 8) hydrogen bonds : bond 0.04724 ( 509) hydrogen bonds : angle 3.97800 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 704 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 807 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 815 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7241 (tp30) REVERT: B 452 TYR cc_start: 0.5521 (OUTLIER) cc_final: 0.5099 (m-10) REVERT: D 767 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7508 (tttm) REVERT: C 704 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8057 (t80) REVERT: C 807 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8358 (tt) REVERT: C 815 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7219 (tp30) outliers start: 60 outliers final: 49 residues processed: 175 average time/residue: 0.1134 time to fit residues: 28.9773 Evaluate side-chains 179 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 414 HIS D 414 HIS C 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.166235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135418 restraints weight = 16981.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126670 restraints weight = 23130.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126405 restraints weight = 21707.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126213 restraints weight = 21215.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126267 restraints weight = 19589.743| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13022 Z= 0.183 Angle : 0.597 10.811 17576 Z= 0.312 Chirality : 0.042 0.154 1958 Planarity : 0.004 0.036 2172 Dihedral : 4.104 18.471 1758 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.08 % Allowed : 27.73 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1614 helix: 1.08 (0.20), residues: 800 sheet: -2.16 (0.39), residues: 174 loop : -2.93 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 677 TYR 0.025 0.002 TYR B 818 PHE 0.020 0.001 PHE C 497 TRP 0.012 0.002 TRP C 580 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00458 (13018) covalent geometry : angle 0.59753 (17568) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.34627 ( 8) hydrogen bonds : bond 0.05475 ( 509) hydrogen bonds : angle 4.08479 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 807 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 815 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7516 (tp30) REVERT: B 415 GLU cc_start: 0.7062 (pm20) cc_final: 0.6722 (mp0) REVERT: B 452 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5325 (m-10) REVERT: D 767 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (tttm) REVERT: C 704 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 807 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8274 (tt) REVERT: C 815 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7521 (tp30) outliers start: 56 outliers final: 48 residues processed: 173 average time/residue: 0.1108 time to fit residues: 28.1420 Evaluate side-chains 178 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 767 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 817 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 138 optimal weight: 0.0470 chunk 137 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143448 restraints weight = 16782.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143352 restraints weight = 30310.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144492 restraints weight = 29485.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144923 restraints weight = 17516.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145601 restraints weight = 15728.468| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13022 Z= 0.111 Angle : 0.557 10.991 17576 Z= 0.290 Chirality : 0.040 0.160 1958 Planarity : 0.003 0.036 2172 Dihedral : 3.892 17.754 1758 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.49 % Allowed : 28.53 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.22), residues: 1614 helix: 1.31 (0.20), residues: 798 sheet: -1.56 (0.46), residues: 142 loop : -2.84 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 677 TYR 0.023 0.001 TYR B 818 PHE 0.013 0.001 PHE D 417 TRP 0.010 0.001 TRP C 580 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00250 (13018) covalent geometry : angle 0.55673 (17568) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.69418 ( 8) hydrogen bonds : bond 0.04164 ( 509) hydrogen bonds : angle 3.87030 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.37 seconds wall clock time: 39 minutes 24.89 seconds (2364.89 seconds total)