Starting phenix.real_space_refine on Mon Jun 16 03:48:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhq_46873/06_2025/9dhq_46873.cif" } resolution = 4.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 128 5.16 5 C 11752 2.51 5 N 2927 2.21 5 O 3262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18069 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3156 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3156 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3203 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Time building chain proxies: 10.70, per 1000 atoms: 0.59 Number of scatterers: 18069 At special positions: 0 Unit cell: (132.89, 115.43, 149.38, 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 128 16.00 O 3262 8.00 N 2927 7.00 C 11752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " 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: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 24 sheets defined 57.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.793A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.528A pdb=" N GLY A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.541A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 572 through 585 removed outlier: 4.261A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 627 removed outlier: 4.532A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 609 " --> pdb=" O TRP A 605 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 623 " --> pdb=" O ASN A 619 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.652A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.833A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.549A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.632A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 818 removed outlier: 4.107A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.821A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.643A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 597 through 620 removed outlier: 3.696A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 4.199A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 675 removed outlier: 4.068A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.774A pdb=" N GLY B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.679A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 814 removed outlier: 3.573A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.615A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 428 " --> pdb=" O TYR C 424 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.562A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.506A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.624A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 572 through 584 removed outlier: 4.436A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 4.264A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 608 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 609 " --> pdb=" O TRP C 605 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 623 " --> pdb=" O ASN C 619 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.536A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.638A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 754 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.552A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.840A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C 804 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 806 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 4.168A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.760A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 542 removed outlier: 3.796A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 620 removed outlier: 3.682A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 removed outlier: 3.653A pdb=" N GLN D 642 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.719A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 662 " --> pdb=" O PHE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 675 removed outlier: 3.632A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 694 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.613A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 743 Processing helix chain 'D' and resid 744 through 756 removed outlier: 3.881A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 769 Processing helix chain 'D' and resid 774 through 778 removed outlier: 3.653A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 817 removed outlier: 3.938A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.666A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR E 13 " --> pdb=" O MET E 9 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 26 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 104 through 122 removed outlier: 4.415A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.498A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 204 removed outlier: 3.960A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 28 removed outlier: 3.914A pdb=" N ILE F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 104 through 116 removed outlier: 4.019A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 133 through 161 removed outlier: 4.120A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE F 149 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY F 161 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 202 removed outlier: 3.906A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.803A pdb=" N THR F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 12 Processing helix chain 'G' and resid 13 through 29 removed outlier: 4.178A pdb=" N PHE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR G 24 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 28 " --> pdb=" O THR G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 105 through 123 removed outlier: 3.704A pdb=" N ALA G 123 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 137 through 160 removed outlier: 3.550A pdb=" N PHE G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 4.048A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP G 202 " --> pdb=" O HIS G 198 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG G 203 " --> pdb=" O MET G 199 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 207 " --> pdb=" O ARG G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.621A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR H 13 " --> pdb=" O MET H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.886A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 161 removed outlier: 4.419A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 152 " --> pdb=" O ASN H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 204 removed outlier: 3.644A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 209 removed outlier: 3.753A pdb=" N GLY H 209 " --> pdb=" O GLN H 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.970A pdb=" N THR A 399 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 398 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 removed outlier: 3.692A pdb=" N ASP A 490 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 736 " --> pdb=" O ASP A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 705 removed outlier: 4.673A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 649 through 650 removed outlier: 7.443A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.300A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.800A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 500 through 501 removed outlier: 3.691A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 703 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 504 through 505 removed outlier: 3.670A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.766A pdb=" N THR C 399 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 398 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 491 removed outlier: 3.532A pdb=" N ASP C 490 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 736 " --> pdb=" O ASP C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 647 removed outlier: 6.550A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.327A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.992A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.617A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.917A pdb=" N SER E 60 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 33 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 174 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC5, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.713A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 33 through 37 847 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5564 1.36 - 1.49: 4901 1.49 - 1.61: 7789 1.61 - 1.74: 1 1.74 - 1.87: 208 Bond restraints: 18463 Sorted by residual: bond pdb=" CB MET A 629 " pdb=" CG MET A 629 " ideal model delta sigma weight residual 1.520 1.692 -0.172 3.00e-02 1.11e+03 3.29e+01 bond pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 1.457 1.524 -0.067 1.29e-02 6.01e+03 2.70e+01 bond pdb=" CA MET A 629 " pdb=" C MET A 629 " ideal model delta sigma weight residual 1.523 1.576 -0.053 1.34e-02 5.57e+03 1.57e+01 bond pdb=" C MET A 629 " pdb=" N VAL A 630 " ideal model delta sigma weight residual 1.332 1.378 -0.046 1.36e-02 5.41e+03 1.15e+01 bond pdb=" C ARG A 628 " pdb=" N MET A 629 " ideal model delta sigma weight residual 1.332 1.380 -0.047 1.40e-02 5.10e+03 1.14e+01 ... (remaining 18458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.68: 24910 9.68 - 19.35: 2 19.35 - 29.03: 4 29.03 - 38.70: 1 38.70 - 48.38: 1 Bond angle restraints: 24918 Sorted by residual: angle pdb=" O ILE A 633 " pdb=" C ILE A 633 " pdb=" N GLU A 634 " ideal model delta sigma weight residual 123.18 152.60 -29.42 1.05e+00 9.07e-01 7.85e+02 angle pdb=" CA ILE A 633 " pdb=" C ILE A 633 " pdb=" N GLU A 634 " ideal model delta sigma weight residual 116.31 88.05 28.26 1.18e+00 7.18e-01 5.73e+02 angle pdb=" CG MET A 629 " pdb=" SD MET A 629 " pdb=" CE MET A 629 " ideal model delta sigma weight residual 100.90 149.28 -48.38 2.20e+00 2.07e-01 4.84e+02 angle pdb=" C ILE A 633 " pdb=" N GLU A 634 " pdb=" CA GLU A 634 " ideal model delta sigma weight residual 122.29 100.03 22.26 1.65e+00 3.67e-01 1.82e+02 angle pdb=" CG MET C 629 " pdb=" SD MET C 629 " pdb=" CE MET C 629 " ideal model delta sigma weight residual 100.90 122.77 -21.87 2.20e+00 2.07e-01 9.88e+01 ... (remaining 24913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 9978 17.56 - 35.13: 718 35.13 - 52.69: 92 52.69 - 70.25: 20 70.25 - 87.82: 14 Dihedral angle restraints: 10822 sinusoidal: 4176 harmonic: 6646 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 143.39 -50.39 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA LYS D 663 " pdb=" C LYS D 663 " pdb=" N ILE D 664 " pdb=" CA ILE D 664 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN D 508 " pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 10819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2153 0.049 - 0.098: 524 0.098 - 0.146: 109 0.146 - 0.195: 8 0.195 - 0.244: 5 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA ARG B 684 " pdb=" N ARG B 684 " pdb=" C ARG B 684 " pdb=" CB ARG B 684 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA SER D 547 " pdb=" N SER D 547 " pdb=" C SER D 547 " pdb=" CB SER D 547 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 645 " pdb=" CA ILE B 645 " pdb=" CG1 ILE B 645 " pdb=" CG2 ILE B 645 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2796 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 453 " 0.297 9.50e-02 1.11e+02 1.34e-01 1.41e+01 pdb=" NE ARG D 453 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 453 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 453 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 453 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 633 " 0.010 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ILE A 633 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 633 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 634 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 533 " -0.002 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR C 533 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR C 533 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 533 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 533 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 533 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 533 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR C 533 " -0.033 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1412 2.74 - 3.28: 19775 3.28 - 3.82: 27691 3.82 - 4.36: 32414 4.36 - 4.90: 53950 Nonbonded interactions: 135242 Sorted by model distance: nonbonded pdb=" OD2 ASP A 638 " pdb=" NE2 GLN A 642 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLU D 416 " pdb=" NH1 ARG D 420 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.243 3.120 nonbonded pdb=" O THR C 480 " pdb=" NH1 ARG C 485 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG B 684 " pdb=" OG1 THR B 685 " model vdw 2.270 3.120 ... (remaining 135237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 817 or (resid \ 818 through 819 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 775 or resid 7 \ 85 through 819)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 817 or (resid \ 818 through 819 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 391 through 775 or resid 785 through 819)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.600 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 0.172 18475 Z= 0.183 Angle : 0.877 48.381 24942 Z= 0.522 Chirality : 0.044 0.244 2799 Planarity : 0.008 0.134 3066 Dihedral : 12.682 87.818 6550 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.68 % Favored : 92.71 % Rotamer: Outliers : 0.16 % Allowed : 1.20 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2276 helix: -1.21 (0.13), residues: 1130 sheet: -1.07 (0.54), residues: 85 loop : -1.50 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 526 HIS 0.002 0.000 HIS G 59 PHE 0.052 0.002 PHE D 546 TYR 0.033 0.004 TYR C 533 ARG 0.031 0.003 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.17471 ( 847) hydrogen bonds : angle 7.05716 ( 2397) SS BOND : bond 0.00232 ( 12) SS BOND : angle 0.96796 ( 24) covalent geometry : bond 0.00327 (18463) covalent geometry : angle 0.87725 (24918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 540 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.9292 (t) cc_final: 0.9072 (m) REVERT: A 403 SER cc_start: 0.8879 (m) cc_final: 0.8482 (p) REVERT: A 421 TYR cc_start: 0.9187 (m-80) cc_final: 0.8980 (m-80) REVERT: A 424 TYR cc_start: 0.8858 (t80) cc_final: 0.8311 (t80) REVERT: A 486 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8445 (mm-30) REVERT: A 491 PHE cc_start: 0.9198 (m-80) cc_final: 0.8304 (m-80) REVERT: A 501 SER cc_start: 0.9004 (t) cc_final: 0.8785 (p) REVERT: A 518 LEU cc_start: 0.9162 (mt) cc_final: 0.8517 (pp) REVERT: A 527 MET cc_start: 0.8534 (tpp) cc_final: 0.8103 (tpp) REVERT: A 633 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7222 (mm) REVERT: A 710 GLU cc_start: 0.8293 (pt0) cc_final: 0.7874 (tt0) REVERT: A 811 LEU cc_start: 0.8489 (mp) cc_final: 0.8182 (mm) REVERT: B 501 SER cc_start: 0.9210 (t) cc_final: 0.8991 (t) REVERT: B 508 GLN cc_start: 0.8671 (pt0) cc_final: 0.8345 (mm-40) REVERT: B 587 GLN cc_start: 0.3700 (mm-40) cc_final: 0.3410 (tp40) REVERT: B 614 SER cc_start: 0.9412 (m) cc_final: 0.9201 (t) REVERT: B 683 VAL cc_start: 0.9036 (m) cc_final: 0.8680 (t) REVERT: B 759 LEU cc_start: 0.9300 (mt) cc_final: 0.9019 (tt) REVERT: C 397 VAL cc_start: 0.9136 (t) cc_final: 0.8816 (m) REVERT: C 407 MET cc_start: 0.8429 (mtp) cc_final: 0.8135 (mmm) REVERT: C 424 TYR cc_start: 0.9151 (t80) cc_final: 0.8751 (t80) REVERT: C 508 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8602 (tp40) REVERT: C 528 CYS cc_start: 0.9314 (m) cc_final: 0.8758 (p) REVERT: C 586 GLN cc_start: 0.7377 (mp10) cc_final: 0.7156 (tt0) REVERT: C 606 TRP cc_start: 0.7406 (m-10) cc_final: 0.6900 (m-10) REVERT: C 668 ASP cc_start: 0.9244 (t0) cc_final: 0.8558 (m-30) REVERT: C 675 ARG cc_start: 0.9310 (ppt170) cc_final: 0.9015 (ptm160) REVERT: C 688 GLU cc_start: 0.9086 (tt0) cc_final: 0.8768 (tt0) REVERT: C 755 GLU cc_start: 0.8164 (tt0) cc_final: 0.7873 (tp30) REVERT: C 797 TYR cc_start: 0.8253 (m-10) cc_final: 0.7890 (t80) REVERT: D 399 THR cc_start: 0.8677 (t) cc_final: 0.8319 (t) REVERT: D 425 CYS cc_start: 0.8393 (m) cc_final: 0.7602 (p) REVERT: D 438 PHE cc_start: 0.7582 (p90) cc_final: 0.7010 (p90) REVERT: D 496 MET cc_start: 0.8741 (ttp) cc_final: 0.8424 (tpp) REVERT: D 578 TRP cc_start: 0.7523 (t-100) cc_final: 0.7303 (t-100) REVERT: D 613 ILE cc_start: 0.9174 (pt) cc_final: 0.8897 (mm) REVERT: D 693 VAL cc_start: 0.9099 (t) cc_final: 0.8479 (p) REVERT: E 14 VAL cc_start: 0.8808 (t) cc_final: 0.8575 (p) REVERT: E 34 TYR cc_start: 0.6965 (m-80) cc_final: 0.6666 (m-80) REVERT: E 140 PHE cc_start: 0.8841 (m-80) cc_final: 0.8581 (m-10) REVERT: E 199 MET cc_start: 0.8378 (mmp) cc_final: 0.7714 (mtp) REVERT: F 131 HIS cc_start: 0.8505 (m-70) cc_final: 0.8301 (m170) REVERT: G 57 MET cc_start: 0.9182 (mmm) cc_final: 0.8582 (mmt) REVERT: G 114 LEU cc_start: 0.8615 (tp) cc_final: 0.8141 (tp) REVERT: G 116 MET cc_start: 0.7309 (mmm) cc_final: 0.7084 (mtt) REVERT: G 140 PHE cc_start: 0.8678 (m-80) cc_final: 0.8087 (m-10) REVERT: G 191 MET cc_start: 0.9134 (mtp) cc_final: 0.8920 (mmp) outliers start: 3 outliers final: 2 residues processed: 543 average time/residue: 0.3161 time to fit residues: 250.8846 Evaluate side-chains 317 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 314 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 93 optimal weight: 0.0270 chunk 180 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093298 restraints weight = 54529.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093137 restraints weight = 48875.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093229 restraints weight = 40481.134| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18475 Z= 0.194 Angle : 0.723 8.981 24942 Z= 0.389 Chirality : 0.045 0.204 2799 Planarity : 0.005 0.049 3066 Dihedral : 6.807 87.331 2498 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 0.21 % Allowed : 3.49 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2276 helix: -0.02 (0.15), residues: 1145 sheet: -1.60 (0.49), residues: 105 loop : -1.13 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 32 HIS 0.009 0.001 HIS G 198 PHE 0.025 0.002 PHE D 546 TYR 0.022 0.002 TYR A 523 ARG 0.007 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 847) hydrogen bonds : angle 5.31721 ( 2397) SS BOND : bond 0.00458 ( 12) SS BOND : angle 1.39431 ( 24) covalent geometry : bond 0.00422 (18463) covalent geometry : angle 0.72215 (24918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 378 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 SER cc_start: 0.8402 (m) cc_final: 0.7923 (p) REVERT: A 424 TYR cc_start: 0.8482 (t80) cc_final: 0.8275 (t80) REVERT: A 474 ILE cc_start: 0.9285 (pt) cc_final: 0.9041 (mp) REVERT: A 491 PHE cc_start: 0.9130 (m-80) cc_final: 0.8412 (m-80) REVERT: A 503 MET cc_start: 0.6918 (tmm) cc_final: 0.6671 (tmm) REVERT: A 518 LEU cc_start: 0.9101 (mt) cc_final: 0.8558 (pp) REVERT: A 527 MET cc_start: 0.8422 (tpp) cc_final: 0.8196 (tpp) REVERT: A 710 GLU cc_start: 0.7835 (pt0) cc_final: 0.7494 (tt0) REVERT: B 508 GLN cc_start: 0.8590 (pt0) cc_final: 0.8292 (mm-40) REVERT: B 587 GLN cc_start: 0.5105 (mm-40) cc_final: 0.4340 (mm-40) REVERT: B 613 ILE cc_start: 0.9450 (pt) cc_final: 0.9196 (mm) REVERT: B 759 LEU cc_start: 0.9447 (mt) cc_final: 0.9059 (tt) REVERT: C 397 VAL cc_start: 0.9387 (t) cc_final: 0.9123 (m) REVERT: C 508 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8497 (tp-100) REVERT: C 528 CYS cc_start: 0.9261 (m) cc_final: 0.8843 (p) REVERT: C 585 MET cc_start: 0.6298 (mtt) cc_final: 0.5976 (mtt) REVERT: C 668 ASP cc_start: 0.9158 (t0) cc_final: 0.8581 (m-30) REVERT: C 674 MET cc_start: 0.7987 (ptm) cc_final: 0.7463 (ttp) REVERT: C 675 ARG cc_start: 0.9163 (ppt170) cc_final: 0.8817 (ptm160) REVERT: D 425 CYS cc_start: 0.8387 (m) cc_final: 0.7355 (p) REVERT: D 533 TYR cc_start: 0.6754 (t80) cc_final: 0.6523 (t80) REVERT: D 693 VAL cc_start: 0.9228 (t) cc_final: 0.8740 (p) REVERT: E 9 MET cc_start: 0.8577 (ppp) cc_final: 0.8326 (ppp) REVERT: E 57 MET cc_start: 0.8635 (mmt) cc_final: 0.8432 (mmp) REVERT: E 116 MET cc_start: 0.7377 (mmm) cc_final: 0.7028 (mtt) REVERT: E 140 PHE cc_start: 0.8538 (m-80) cc_final: 0.7875 (m-10) REVERT: E 188 ILE cc_start: 0.8758 (tp) cc_final: 0.8479 (tt) REVERT: E 199 MET cc_start: 0.8464 (mmp) cc_final: 0.7766 (mtp) REVERT: F 32 TRP cc_start: 0.6911 (m-10) cc_final: 0.6531 (m-10) REVERT: G 9 MET cc_start: 0.8548 (mtm) cc_final: 0.8061 (mtt) REVERT: G 106 PHE cc_start: 0.8734 (m-80) cc_final: 0.8246 (m-80) REVERT: G 148 ASN cc_start: 0.8920 (m-40) cc_final: 0.8532 (m110) REVERT: H 130 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6823 (mmp-170) outliers start: 4 outliers final: 0 residues processed: 382 average time/residue: 0.3078 time to fit residues: 175.1980 Evaluate side-chains 259 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS F 59 HIS F 131 HIS ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093898 restraints weight = 54818.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094148 restraints weight = 47958.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093972 restraints weight = 40761.176| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18475 Z= 0.167 Angle : 0.662 9.299 24942 Z= 0.355 Chirality : 0.043 0.176 2799 Planarity : 0.004 0.051 3066 Dihedral : 6.324 84.696 2498 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2276 helix: 0.21 (0.15), residues: 1147 sheet: -1.44 (0.55), residues: 95 loop : -1.15 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 578 HIS 0.010 0.001 HIS G 198 PHE 0.041 0.002 PHE C 574 TYR 0.018 0.002 TYR F 127 ARG 0.015 0.001 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 847) hydrogen bonds : angle 4.93012 ( 2397) SS BOND : bond 0.00358 ( 12) SS BOND : angle 1.26036 ( 24) covalent geometry : bond 0.00366 (18463) covalent geometry : angle 0.66162 (24918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.9144 (m-80) cc_final: 0.8698 (m-80) REVERT: A 503 MET cc_start: 0.7065 (tmm) cc_final: 0.6844 (tmm) REVERT: A 518 LEU cc_start: 0.9190 (mt) cc_final: 0.8622 (pp) REVERT: A 527 MET cc_start: 0.8290 (tpp) cc_final: 0.8035 (tpp) REVERT: A 585 MET cc_start: 0.6113 (mmm) cc_final: 0.5862 (mmt) REVERT: A 710 GLU cc_start: 0.7856 (pt0) cc_final: 0.7622 (tt0) REVERT: B 503 MET cc_start: 0.9224 (ppp) cc_final: 0.8989 (ppp) REVERT: B 508 GLN cc_start: 0.8590 (pt0) cc_final: 0.8220 (mm-40) REVERT: B 587 GLN cc_start: 0.5461 (mm-40) cc_final: 0.4656 (mm-40) REVERT: B 759 LEU cc_start: 0.9480 (mt) cc_final: 0.9105 (tt) REVERT: C 397 VAL cc_start: 0.9403 (t) cc_final: 0.9129 (m) REVERT: C 486 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8117 (mt-10) REVERT: C 508 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8417 (tp-100) REVERT: C 528 CYS cc_start: 0.9330 (m) cc_final: 0.8750 (p) REVERT: C 674 MET cc_start: 0.8022 (ptm) cc_final: 0.7750 (ttp) REVERT: C 675 ARG cc_start: 0.9253 (ppt170) cc_final: 0.8961 (ptm160) REVERT: D 425 CYS cc_start: 0.8381 (m) cc_final: 0.7940 (p) REVERT: D 431 GLU cc_start: 0.9032 (mp0) cc_final: 0.8820 (mp0) REVERT: D 503 MET cc_start: 0.8940 (ppp) cc_final: 0.8610 (ppp) REVERT: E 9 MET cc_start: 0.8566 (ppp) cc_final: 0.8290 (ppp) REVERT: E 34 TYR cc_start: 0.7703 (m-80) cc_final: 0.7445 (m-10) REVERT: E 116 MET cc_start: 0.7303 (mmm) cc_final: 0.7001 (mtt) REVERT: E 140 PHE cc_start: 0.8541 (m-80) cc_final: 0.7811 (m-10) REVERT: E 146 LEU cc_start: 0.9220 (tp) cc_final: 0.8996 (tp) REVERT: E 188 ILE cc_start: 0.8612 (tp) cc_final: 0.7987 (tp) REVERT: E 199 MET cc_start: 0.8416 (mmp) cc_final: 0.7726 (ttm) REVERT: F 32 TRP cc_start: 0.6911 (m-10) cc_final: 0.6663 (m-10) REVERT: G 69 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.3344 (pm20) REVERT: G 106 PHE cc_start: 0.8723 (m-80) cc_final: 0.8239 (m-80) REVERT: G 112 ILE cc_start: 0.7121 (tt) cc_final: 0.6886 (tt) REVERT: G 148 ASN cc_start: 0.8909 (m-40) cc_final: 0.8510 (m-40) REVERT: G 191 MET cc_start: 0.8865 (ptt) cc_final: 0.8517 (mmp) REVERT: H 187 ILE cc_start: 0.8469 (mm) cc_final: 0.8229 (pt) REVERT: H 191 MET cc_start: 0.6907 (mmt) cc_final: 0.6700 (mmm) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.3044 time to fit residues: 152.5206 Evaluate side-chains 256 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 19 optimal weight: 8.9990 chunk 139 optimal weight: 0.0570 chunk 226 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 213 optimal weight: 10.0000 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094549 restraints weight = 55370.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094851 restraints weight = 49091.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095011 restraints weight = 39780.803| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18475 Z= 0.156 Angle : 0.642 8.699 24942 Z= 0.341 Chirality : 0.043 0.232 2799 Planarity : 0.004 0.049 3066 Dihedral : 6.057 82.833 2498 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2276 helix: 0.34 (0.15), residues: 1146 sheet: -1.35 (0.51), residues: 110 loop : -1.26 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 578 HIS 0.007 0.001 HIS G 59 PHE 0.034 0.002 PHE A 574 TYR 0.019 0.001 TYR F 127 ARG 0.007 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 847) hydrogen bonds : angle 4.74252 ( 2397) SS BOND : bond 0.00369 ( 12) SS BOND : angle 1.16790 ( 24) covalent geometry : bond 0.00341 (18463) covalent geometry : angle 0.64083 (24918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.9124 (m-80) cc_final: 0.8299 (m-10) REVERT: A 518 LEU cc_start: 0.9221 (mt) cc_final: 0.8628 (pp) REVERT: A 527 MET cc_start: 0.8268 (tpp) cc_final: 0.8001 (tpp) REVERT: B 503 MET cc_start: 0.9255 (ppp) cc_final: 0.8865 (ppp) REVERT: B 508 GLN cc_start: 0.8525 (pt0) cc_final: 0.8183 (mm-40) REVERT: B 587 GLN cc_start: 0.5774 (mm-40) cc_final: 0.4824 (mm-40) REVERT: B 670 MET cc_start: 0.8258 (mmp) cc_final: 0.7958 (mmp) REVERT: B 759 LEU cc_start: 0.9494 (mt) cc_final: 0.9133 (tt) REVERT: C 397 VAL cc_start: 0.9376 (t) cc_final: 0.9075 (m) REVERT: C 503 MET cc_start: 0.7803 (tpp) cc_final: 0.7499 (tpp) REVERT: C 508 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8416 (tp-100) REVERT: C 545 ARG cc_start: 0.6760 (mmt180) cc_final: 0.6356 (mmt180) REVERT: C 675 ARG cc_start: 0.9209 (ppt170) cc_final: 0.8994 (ptm160) REVERT: C 710 GLU cc_start: 0.8086 (pp20) cc_final: 0.7829 (pp20) REVERT: D 425 CYS cc_start: 0.8581 (m) cc_final: 0.7910 (p) REVERT: D 503 MET cc_start: 0.8875 (ppp) cc_final: 0.8611 (ppp) REVERT: D 527 MET cc_start: 0.6539 (mmt) cc_final: 0.6338 (mmt) REVERT: E 9 MET cc_start: 0.8550 (ppp) cc_final: 0.8245 (ppp) REVERT: E 34 TYR cc_start: 0.7767 (m-80) cc_final: 0.7519 (m-10) REVERT: E 116 MET cc_start: 0.7224 (mmm) cc_final: 0.6964 (mtt) REVERT: E 140 PHE cc_start: 0.8412 (m-80) cc_final: 0.7719 (m-80) REVERT: E 146 LEU cc_start: 0.9214 (tp) cc_final: 0.8943 (tp) REVERT: E 188 ILE cc_start: 0.8560 (tp) cc_final: 0.8352 (tp) REVERT: E 199 MET cc_start: 0.8319 (mmp) cc_final: 0.7647 (ttm) REVERT: F 29 THR cc_start: 0.9317 (p) cc_final: 0.9063 (t) REVERT: F 32 TRP cc_start: 0.6807 (m-10) cc_final: 0.6607 (m-10) REVERT: F 101 ARG cc_start: 0.8467 (tpt-90) cc_final: 0.8255 (tpt-90) REVERT: G 106 PHE cc_start: 0.8647 (m-80) cc_final: 0.8226 (m-80) REVERT: G 112 ILE cc_start: 0.7641 (tt) cc_final: 0.7018 (tt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.3029 time to fit residues: 152.0227 Evaluate side-chains 254 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 79 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 47 optimal weight: 0.0870 chunk 87 optimal weight: 0.0000 chunk 143 optimal weight: 0.0970 chunk 189 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096247 restraints weight = 55027.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096151 restraints weight = 50082.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096738 restraints weight = 39597.245| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18475 Z= 0.122 Angle : 0.603 10.070 24942 Z= 0.318 Chirality : 0.041 0.169 2799 Planarity : 0.004 0.047 3066 Dihedral : 5.605 79.864 2498 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2276 helix: 0.55 (0.15), residues: 1162 sheet: -1.50 (0.48), residues: 120 loop : -1.20 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 32 HIS 0.007 0.001 HIS G 198 PHE 0.034 0.001 PHE A 574 TYR 0.013 0.001 TYR C 673 ARG 0.004 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 847) hydrogen bonds : angle 4.44926 ( 2397) SS BOND : bond 0.00532 ( 12) SS BOND : angle 1.53565 ( 24) covalent geometry : bond 0.00260 (18463) covalent geometry : angle 0.60134 (24918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.9085 (m-80) cc_final: 0.8134 (m-10) REVERT: A 518 LEU cc_start: 0.9198 (mt) cc_final: 0.8557 (pp) REVERT: B 503 MET cc_start: 0.9262 (ppp) cc_final: 0.8819 (ppp) REVERT: B 508 GLN cc_start: 0.8471 (pt0) cc_final: 0.8114 (mm-40) REVERT: B 578 TRP cc_start: 0.7111 (t-100) cc_final: 0.6888 (t60) REVERT: B 587 GLN cc_start: 0.5773 (mm-40) cc_final: 0.5438 (mp10) REVERT: B 670 MET cc_start: 0.8230 (mmp) cc_final: 0.7992 (mmm) REVERT: B 759 LEU cc_start: 0.9506 (mt) cc_final: 0.9145 (tt) REVERT: C 397 VAL cc_start: 0.9289 (t) cc_final: 0.8908 (m) REVERT: C 503 MET cc_start: 0.7999 (tpp) cc_final: 0.7503 (tpp) REVERT: C 508 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8395 (tp-100) REVERT: C 670 MET cc_start: 0.9215 (ptm) cc_final: 0.8920 (ptm) REVERT: C 674 MET cc_start: 0.8654 (ptp) cc_final: 0.7334 (ttm) REVERT: D 425 CYS cc_start: 0.8572 (m) cc_final: 0.7896 (p) REVERT: D 527 MET cc_start: 0.6557 (mmt) cc_final: 0.6281 (mmt) REVERT: D 721 MET cc_start: 0.8557 (ppp) cc_final: 0.8353 (ppp) REVERT: E 9 MET cc_start: 0.8516 (ppp) cc_final: 0.8112 (ppp) REVERT: E 34 TYR cc_start: 0.7701 (m-80) cc_final: 0.7463 (m-10) REVERT: E 116 MET cc_start: 0.7179 (mmm) cc_final: 0.6724 (mtt) REVERT: E 140 PHE cc_start: 0.8405 (m-80) cc_final: 0.7761 (m-80) REVERT: E 146 LEU cc_start: 0.9210 (tp) cc_final: 0.8968 (tp) REVERT: E 188 ILE cc_start: 0.8599 (tp) cc_final: 0.8363 (tt) REVERT: E 199 MET cc_start: 0.8297 (mmp) cc_final: 0.7686 (ttm) REVERT: F 29 THR cc_start: 0.9310 (p) cc_final: 0.9103 (t) REVERT: F 32 TRP cc_start: 0.6866 (m-10) cc_final: 0.6651 (m-10) REVERT: F 57 MET cc_start: 0.7485 (mmp) cc_final: 0.6763 (mmp) REVERT: F 101 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8240 (tpt-90) REVERT: F 203 ARG cc_start: 0.8666 (mtt90) cc_final: 0.8438 (mtt90) REVERT: G 106 PHE cc_start: 0.8647 (m-80) cc_final: 0.8272 (m-10) REVERT: G 112 ILE cc_start: 0.7633 (tt) cc_final: 0.7164 (tt) REVERT: G 140 PHE cc_start: 0.8100 (m-10) cc_final: 0.7863 (m-10) REVERT: H 191 MET cc_start: 0.7561 (mmp) cc_final: 0.7338 (mmm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3042 time to fit residues: 153.6590 Evaluate side-chains 255 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 211 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 89 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096490 restraints weight = 53914.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096731 restraints weight = 46850.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096954 restraints weight = 37267.887| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18475 Z= 0.121 Angle : 0.584 10.054 24942 Z= 0.308 Chirality : 0.041 0.210 2799 Planarity : 0.004 0.045 3066 Dihedral : 5.327 75.326 2498 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.18 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2276 helix: 0.71 (0.15), residues: 1166 sheet: -1.47 (0.46), residues: 131 loop : -1.13 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 63 HIS 0.004 0.001 HIS G 198 PHE 0.028 0.001 PHE A 574 TYR 0.019 0.001 TYR A 523 ARG 0.010 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 847) hydrogen bonds : angle 4.32458 ( 2397) SS BOND : bond 0.00398 ( 12) SS BOND : angle 1.29788 ( 24) covalent geometry : bond 0.00260 (18463) covalent geometry : angle 0.58299 (24918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7534 (tp30) REVERT: A 518 LEU cc_start: 0.9265 (mt) cc_final: 0.8547 (pp) REVERT: B 503 MET cc_start: 0.9249 (ppp) cc_final: 0.8953 (ppp) REVERT: B 508 GLN cc_start: 0.8437 (pt0) cc_final: 0.8038 (mm-40) REVERT: B 587 GLN cc_start: 0.5743 (mm-40) cc_final: 0.5541 (mp10) REVERT: C 397 VAL cc_start: 0.9429 (t) cc_final: 0.9094 (m) REVERT: C 503 MET cc_start: 0.8196 (tpp) cc_final: 0.7669 (tpp) REVERT: C 670 MET cc_start: 0.9259 (ptm) cc_final: 0.8915 (ptm) REVERT: C 674 MET cc_start: 0.8577 (ptp) cc_final: 0.7389 (ttm) REVERT: C 710 GLU cc_start: 0.8160 (pp20) cc_final: 0.7861 (pp20) REVERT: D 527 MET cc_start: 0.6773 (mmt) cc_final: 0.6403 (mmt) REVERT: D 533 TYR cc_start: 0.6703 (t80) cc_final: 0.6437 (t80) REVERT: D 813 GLU cc_start: 0.8405 (tt0) cc_final: 0.7740 (tp30) REVERT: E 9 MET cc_start: 0.8526 (ppp) cc_final: 0.8106 (ppp) REVERT: E 116 MET cc_start: 0.7123 (mmm) cc_final: 0.6635 (mtt) REVERT: E 140 PHE cc_start: 0.8346 (m-80) cc_final: 0.7743 (m-80) REVERT: E 146 LEU cc_start: 0.9258 (tp) cc_final: 0.9021 (tp) REVERT: E 191 MET cc_start: 0.8547 (ppp) cc_final: 0.8237 (tpp) REVERT: E 199 MET cc_start: 0.8280 (mmp) cc_final: 0.7665 (mtp) REVERT: F 66 CYS cc_start: 0.6301 (m) cc_final: 0.6031 (t) REVERT: F 101 ARG cc_start: 0.8373 (tpt-90) cc_final: 0.8048 (tpt-90) REVERT: F 203 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8438 (mtt90) REVERT: G 101 ARG cc_start: 0.8960 (tpt170) cc_final: 0.8336 (tpm170) REVERT: G 106 PHE cc_start: 0.8603 (m-80) cc_final: 0.8264 (m-10) REVERT: G 112 ILE cc_start: 0.7957 (tt) cc_final: 0.7434 (tt) REVERT: H 59 HIS cc_start: 0.3222 (p90) cc_final: 0.2812 (p90) REVERT: H 191 MET cc_start: 0.7720 (mmp) cc_final: 0.7465 (mmm) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.2969 time to fit residues: 148.7331 Evaluate side-chains 251 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 64 optimal weight: 2.9990 chunk 162 optimal weight: 0.0470 chunk 209 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097717 restraints weight = 54798.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097489 restraints weight = 48485.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097729 restraints weight = 39381.934| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18475 Z= 0.120 Angle : 0.605 12.173 24942 Z= 0.313 Chirality : 0.041 0.183 2799 Planarity : 0.004 0.044 3066 Dihedral : 5.139 72.044 2498 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2276 helix: 0.78 (0.15), residues: 1161 sheet: -1.48 (0.47), residues: 131 loop : -1.11 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 578 HIS 0.004 0.001 HIS G 198 PHE 0.030 0.001 PHE A 531 TYR 0.019 0.001 TYR C 421 ARG 0.025 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 847) hydrogen bonds : angle 4.33142 ( 2397) SS BOND : bond 0.00247 ( 12) SS BOND : angle 0.91262 ( 24) covalent geometry : bond 0.00257 (18463) covalent geometry : angle 0.60449 (24918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7505 (tp30) REVERT: A 491 PHE cc_start: 0.9085 (m-80) cc_final: 0.8728 (m-10) REVERT: A 518 LEU cc_start: 0.9260 (mt) cc_final: 0.8488 (pp) REVERT: B 503 MET cc_start: 0.9239 (ppp) cc_final: 0.8916 (ppp) REVERT: B 508 GLN cc_start: 0.8474 (pt0) cc_final: 0.8036 (mm-40) REVERT: C 397 VAL cc_start: 0.9400 (t) cc_final: 0.9014 (m) REVERT: C 402 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7380 (tm-30) REVERT: C 670 MET cc_start: 0.9230 (ptm) cc_final: 0.8889 (ptm) REVERT: C 674 MET cc_start: 0.8523 (ptp) cc_final: 0.7648 (ttp) REVERT: C 811 LEU cc_start: 0.8064 (mm) cc_final: 0.7570 (mm) REVERT: D 527 MET cc_start: 0.6941 (mmt) cc_final: 0.6454 (mmt) REVERT: D 707 THR cc_start: 0.9881 (p) cc_final: 0.9609 (t) REVERT: D 813 GLU cc_start: 0.8391 (tt0) cc_final: 0.7712 (tp30) REVERT: E 9 MET cc_start: 0.8407 (ppp) cc_final: 0.7975 (ppp) REVERT: E 116 MET cc_start: 0.7095 (mmm) cc_final: 0.6563 (mtt) REVERT: E 140 PHE cc_start: 0.8303 (m-80) cc_final: 0.7771 (m-80) REVERT: E 146 LEU cc_start: 0.9272 (tp) cc_final: 0.9022 (tp) REVERT: E 188 ILE cc_start: 0.8520 (tp) cc_final: 0.8181 (tt) REVERT: E 199 MET cc_start: 0.8215 (mmp) cc_final: 0.7660 (mtp) REVERT: F 101 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.8050 (tpt-90) REVERT: F 203 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8411 (mtt90) REVERT: G 106 PHE cc_start: 0.8603 (m-80) cc_final: 0.8326 (m-10) REVERT: G 112 ILE cc_start: 0.8221 (tt) cc_final: 0.7677 (tt) REVERT: G 191 MET cc_start: 0.7682 (mmp) cc_final: 0.7481 (mmp) REVERT: H 59 HIS cc_start: 0.2996 (p90) cc_final: 0.2520 (p90) REVERT: H 130 ARG cc_start: 0.6749 (mtt180) cc_final: 0.6478 (mmp-170) REVERT: H 191 MET cc_start: 0.7687 (mmp) cc_final: 0.7433 (mmm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2926 time to fit residues: 149.2706 Evaluate side-chains 247 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 152 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 392 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.120394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095988 restraints weight = 54938.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095844 restraints weight = 47474.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096724 restraints weight = 38851.978| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18475 Z= 0.136 Angle : 0.621 11.184 24942 Z= 0.321 Chirality : 0.042 0.203 2799 Planarity : 0.004 0.044 3066 Dihedral : 5.103 67.865 2498 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2276 helix: 0.82 (0.16), residues: 1161 sheet: -1.57 (0.46), residues: 130 loop : -1.18 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 578 HIS 0.004 0.001 HIS G 59 PHE 0.027 0.001 PHE A 574 TYR 0.021 0.001 TYR A 421 ARG 0.006 0.000 ARG E 101 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 847) hydrogen bonds : angle 4.36811 ( 2397) SS BOND : bond 0.00613 ( 12) SS BOND : angle 0.95414 ( 24) covalent geometry : bond 0.00298 (18463) covalent geometry : angle 0.62014 (24918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7432 (tp30) REVERT: A 518 LEU cc_start: 0.9213 (mt) cc_final: 0.8641 (pp) REVERT: A 527 MET cc_start: 0.8398 (tpp) cc_final: 0.8121 (tpp) REVERT: B 503 MET cc_start: 0.9290 (ppp) cc_final: 0.8997 (ppp) REVERT: B 508 GLN cc_start: 0.8336 (pt0) cc_final: 0.7997 (mm-40) REVERT: B 578 TRP cc_start: 0.7236 (t-100) cc_final: 0.6281 (t60) REVERT: B 670 MET cc_start: 0.8057 (mmp) cc_final: 0.7716 (mmp) REVERT: C 397 VAL cc_start: 0.9348 (t) cc_final: 0.8953 (m) REVERT: C 407 MET cc_start: 0.8981 (mmm) cc_final: 0.8663 (mmm) REVERT: C 668 ASP cc_start: 0.9219 (t0) cc_final: 0.8363 (m-30) REVERT: C 670 MET cc_start: 0.9244 (ptm) cc_final: 0.8851 (ptm) REVERT: C 674 MET cc_start: 0.8492 (ptp) cc_final: 0.7495 (ttp) REVERT: C 811 LEU cc_start: 0.7926 (mm) cc_final: 0.7454 (mm) REVERT: D 425 CYS cc_start: 0.8599 (m) cc_final: 0.7869 (p) REVERT: D 813 GLU cc_start: 0.8310 (tt0) cc_final: 0.7652 (tp30) REVERT: E 9 MET cc_start: 0.8388 (ppp) cc_final: 0.7959 (ppp) REVERT: E 116 MET cc_start: 0.7069 (mmm) cc_final: 0.6420 (mtt) REVERT: E 140 PHE cc_start: 0.8274 (m-80) cc_final: 0.7679 (m-80) REVERT: E 188 ILE cc_start: 0.8480 (tp) cc_final: 0.8105 (tt) REVERT: E 190 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8565 (mp0) REVERT: E 199 MET cc_start: 0.8109 (mmp) cc_final: 0.7602 (mtp) REVERT: F 101 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7969 (tpt-90) REVERT: F 203 ARG cc_start: 0.8670 (mtt90) cc_final: 0.8356 (mtt90) REVERT: G 101 ARG cc_start: 0.9030 (tpt170) cc_final: 0.8517 (tpm170) REVERT: G 106 PHE cc_start: 0.8647 (m-80) cc_final: 0.8345 (m-10) REVERT: G 112 ILE cc_start: 0.8225 (tt) cc_final: 0.7835 (tt) REVERT: G 148 ASN cc_start: 0.8892 (m-40) cc_final: 0.8444 (m-40) REVERT: G 192 VAL cc_start: 0.9151 (t) cc_final: 0.8933 (t) REVERT: H 130 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6524 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2949 time to fit residues: 140.9969 Evaluate side-chains 241 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095335 restraints weight = 55293.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095292 restraints weight = 47543.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096453 restraints weight = 38568.850| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18475 Z= 0.156 Angle : 0.653 13.491 24942 Z= 0.338 Chirality : 0.043 0.177 2799 Planarity : 0.004 0.047 3066 Dihedral : 5.108 63.772 2498 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2276 helix: 0.77 (0.16), residues: 1167 sheet: -1.42 (0.45), residues: 141 loop : -1.18 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 578 HIS 0.005 0.001 HIS H 59 PHE 0.047 0.002 PHE C 574 TYR 0.021 0.001 TYR A 523 ARG 0.006 0.000 ARG E 101 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 847) hydrogen bonds : angle 4.47548 ( 2397) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.10010 ( 24) covalent geometry : bond 0.00347 (18463) covalent geometry : angle 0.65281 (24918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7461 (tp30) REVERT: A 518 LEU cc_start: 0.9197 (mt) cc_final: 0.8634 (pp) REVERT: A 527 MET cc_start: 0.8443 (tpp) cc_final: 0.8097 (tpp) REVERT: A 545 ARG cc_start: 0.6764 (mmt-90) cc_final: 0.6450 (mmt180) REVERT: B 503 MET cc_start: 0.9280 (ppp) cc_final: 0.9021 (ppp) REVERT: B 508 GLN cc_start: 0.8301 (pt0) cc_final: 0.7925 (mm-40) REVERT: B 578 TRP cc_start: 0.7139 (t-100) cc_final: 0.6360 (t60) REVERT: B 670 MET cc_start: 0.8130 (mmp) cc_final: 0.7779 (mmp) REVERT: C 397 VAL cc_start: 0.9384 (t) cc_final: 0.9004 (m) REVERT: C 402 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6802 (tm-30) REVERT: C 407 MET cc_start: 0.9015 (mmm) cc_final: 0.8639 (mmm) REVERT: C 668 ASP cc_start: 0.9226 (t0) cc_final: 0.8363 (m-30) REVERT: C 670 MET cc_start: 0.9234 (ptm) cc_final: 0.8950 (ptm) REVERT: C 674 MET cc_start: 0.8634 (ptp) cc_final: 0.7547 (ttp) REVERT: C 811 LEU cc_start: 0.7951 (mm) cc_final: 0.7490 (mm) REVERT: D 425 CYS cc_start: 0.8669 (m) cc_final: 0.7890 (p) REVERT: D 721 MET cc_start: 0.9194 (ptm) cc_final: 0.8389 (ppp) REVERT: D 769 ASP cc_start: 0.8791 (m-30) cc_final: 0.8556 (m-30) REVERT: D 813 GLU cc_start: 0.8344 (tt0) cc_final: 0.7696 (tp30) REVERT: E 9 MET cc_start: 0.8383 (ppp) cc_final: 0.7884 (ppp) REVERT: E 116 MET cc_start: 0.7102 (mmm) cc_final: 0.6469 (mtt) REVERT: E 140 PHE cc_start: 0.8292 (m-80) cc_final: 0.7790 (m-80) REVERT: E 188 ILE cc_start: 0.8436 (tp) cc_final: 0.8081 (tt) REVERT: E 190 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8538 (mp0) REVERT: E 199 MET cc_start: 0.8107 (mmp) cc_final: 0.7598 (mtp) REVERT: F 101 ARG cc_start: 0.8348 (tpt-90) cc_final: 0.8001 (tpt-90) REVERT: G 24 THR cc_start: 0.8953 (t) cc_final: 0.8729 (p) REVERT: G 101 ARG cc_start: 0.9106 (tpt170) cc_final: 0.8853 (tpt90) REVERT: G 112 ILE cc_start: 0.8027 (tt) cc_final: 0.7629 (tt) REVERT: G 148 ASN cc_start: 0.8820 (m-40) cc_final: 0.8424 (m-40) REVERT: H 130 ARG cc_start: 0.6727 (mtt180) cc_final: 0.6524 (mmp-170) REVERT: H 131 HIS cc_start: 0.7910 (m-70) cc_final: 0.7693 (m-70) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2851 time to fit residues: 138.6275 Evaluate side-chains 236 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 37 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 109 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 392 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097916 restraints weight = 54571.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097980 restraints weight = 45777.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098887 restraints weight = 36691.756| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18475 Z= 0.116 Angle : 0.616 11.827 24942 Z= 0.316 Chirality : 0.041 0.215 2799 Planarity : 0.004 0.046 3066 Dihedral : 4.800 57.800 2498 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2276 helix: 0.84 (0.16), residues: 1166 sheet: -1.40 (0.42), residues: 158 loop : -1.16 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 606 HIS 0.005 0.001 HIS H 59 PHE 0.047 0.001 PHE C 574 TYR 0.020 0.001 TYR C 702 ARG 0.018 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 847) hydrogen bonds : angle 4.28696 ( 2397) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.20112 ( 24) covalent geometry : bond 0.00248 (18463) covalent geometry : angle 0.61535 (24918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8576 (m-80) cc_final: 0.7616 (m-80) REVERT: A 431 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7364 (tp30) REVERT: A 491 PHE cc_start: 0.8615 (m-80) cc_final: 0.8246 (m-10) REVERT: A 503 MET cc_start: 0.6939 (tmm) cc_final: 0.6739 (tmm) REVERT: A 518 LEU cc_start: 0.9208 (mt) cc_final: 0.8561 (pp) REVERT: A 545 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.6453 (mmt180) REVERT: B 414 MET cc_start: 0.7621 (pmm) cc_final: 0.7325 (pmm) REVERT: B 503 MET cc_start: 0.9242 (ppp) cc_final: 0.8997 (ppp) REVERT: B 508 GLN cc_start: 0.8131 (pt0) cc_final: 0.7832 (mm-40) REVERT: B 670 MET cc_start: 0.8142 (mmp) cc_final: 0.7755 (mmp) REVERT: B 769 ASP cc_start: 0.8456 (m-30) cc_final: 0.8224 (m-30) REVERT: C 393 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7220 (mmtt) REVERT: C 397 VAL cc_start: 0.9346 (t) cc_final: 0.8977 (m) REVERT: C 402 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6594 (tm-30) REVERT: C 407 MET cc_start: 0.8987 (mmm) cc_final: 0.8603 (mmm) REVERT: C 432 ILE cc_start: 0.9430 (mm) cc_final: 0.8982 (mm) REVERT: C 668 ASP cc_start: 0.9009 (t70) cc_final: 0.8414 (m-30) REVERT: C 670 MET cc_start: 0.9200 (ptm) cc_final: 0.8906 (ptm) REVERT: C 674 MET cc_start: 0.8617 (ptp) cc_final: 0.7536 (ttp) REVERT: D 425 CYS cc_start: 0.8474 (m) cc_final: 0.7825 (p) REVERT: D 533 TYR cc_start: 0.6600 (t80) cc_final: 0.6389 (t80) REVERT: D 721 MET cc_start: 0.9172 (ptm) cc_final: 0.8404 (ppp) REVERT: D 769 ASP cc_start: 0.8806 (m-30) cc_final: 0.7719 (t0) REVERT: D 813 GLU cc_start: 0.8318 (tt0) cc_final: 0.7739 (tp30) REVERT: E 9 MET cc_start: 0.8354 (ppp) cc_final: 0.7826 (ppp) REVERT: E 116 MET cc_start: 0.7046 (mmm) cc_final: 0.6352 (mtt) REVERT: E 140 PHE cc_start: 0.8263 (m-80) cc_final: 0.7669 (m-80) REVERT: E 188 ILE cc_start: 0.8431 (tp) cc_final: 0.8071 (tt) REVERT: E 190 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8533 (mp0) REVERT: E 199 MET cc_start: 0.8179 (mmp) cc_final: 0.7613 (mtp) REVERT: F 101 ARG cc_start: 0.8301 (tpt-90) cc_final: 0.8089 (tpt-90) REVERT: G 98 ARG cc_start: 0.8749 (ptp-110) cc_final: 0.8472 (ptp-170) REVERT: G 112 ILE cc_start: 0.7888 (tt) cc_final: 0.7576 (tt) REVERT: G 148 ASN cc_start: 0.8848 (m-40) cc_final: 0.8425 (m-40) REVERT: G 191 MET cc_start: 0.7731 (mmp) cc_final: 0.7525 (mmt) REVERT: H 131 HIS cc_start: 0.7796 (m-70) cc_final: 0.7583 (m-70) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2875 time to fit residues: 136.4662 Evaluate side-chains 243 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 213 optimal weight: 0.1980 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 392 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096643 restraints weight = 54691.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096498 restraints weight = 46598.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097534 restraints weight = 38119.236| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18475 Z= 0.134 Angle : 0.623 11.953 24942 Z= 0.320 Chirality : 0.042 0.265 2799 Planarity : 0.004 0.061 3066 Dihedral : 4.799 52.110 2498 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2276 helix: 0.87 (0.16), residues: 1169 sheet: -1.37 (0.42), residues: 158 loop : -1.21 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 606 HIS 0.005 0.001 HIS H 59 PHE 0.044 0.001 PHE C 574 TYR 0.023 0.001 TYR A 523 ARG 0.009 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 847) hydrogen bonds : angle 4.30860 ( 2397) SS BOND : bond 0.00246 ( 12) SS BOND : angle 1.08715 ( 24) covalent geometry : bond 0.00297 (18463) covalent geometry : angle 0.62216 (24918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5508.11 seconds wall clock time: 96 minutes 30.89 seconds (5790.89 seconds total)