Starting phenix.real_space_refine on Thu Sep 18 16:06:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhq_46873/09_2025/9dhq_46873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhq_46873/09_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_46873/09_2025/9dhq_46873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhq_46873/09_2025/9dhq_46873.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhq_46873/09_2025/9dhq_46873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhq_46873/09_2025/9dhq_46873.cif" } resolution = 4.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.60, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 861.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.71 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: 4.12 Time building geometry restraints manager: 2.22 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.440 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 : 3.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.031 0.003 ARG D 453 TYR 0.033 0.004 TYR C 533 PHE 0.052 0.002 PHE D 546 TRP 0.035 0.002 TRP C 526 HIS 0.002 0.000 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00327 (18463) covalent geometry : angle 0.87725 (24918) SS BOND : bond 0.00232 ( 12) SS BOND : angle 0.96796 ( 24) hydrogen bonds : bond 0.17471 ( 847) hydrogen bonds : angle 7.05716 ( 2397) *********************** 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 : 0.641 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: 0.1596 time to fit residues: 126.3372 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 709 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN F 148 ASN ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092803 restraints weight = 54924.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092326 restraints weight = 47017.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093102 restraints weight = 39799.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093406 restraints weight = 33544.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093486 restraints weight = 31059.327| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18475 Z= 0.234 Angle : 0.748 9.674 24942 Z= 0.405 Chirality : 0.045 0.226 2799 Planarity : 0.005 0.055 3066 Dihedral : 7.037 87.653 2498 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 0.31 % Allowed : 3.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2276 helix: -0.13 (0.15), residues: 1141 sheet: -1.55 (0.50), residues: 104 loop : -1.20 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 98 TYR 0.023 0.002 TYR A 523 PHE 0.027 0.002 PHE D 546 TRP 0.021 0.002 TRP G 32 HIS 0.009 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00512 (18463) covalent geometry : angle 0.74685 (24918) SS BOND : bond 0.00676 ( 12) SS BOND : angle 1.55753 ( 24) hydrogen bonds : bond 0.05788 ( 847) hydrogen bonds : angle 5.57693 ( 2397) *********************** 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 371 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 365 time to evaluate : 0.757 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: A 403 SER cc_start: 0.8485 (m) cc_final: 0.7988 (p) REVERT: A 424 TYR cc_start: 0.8527 (t80) cc_final: 0.8293 (t80) REVERT: A 491 PHE cc_start: 0.9088 (m-80) cc_final: 0.8387 (m-80) REVERT: A 518 LEU cc_start: 0.9125 (mt) cc_final: 0.8611 (pp) REVERT: A 681 VAL cc_start: 0.8920 (p) cc_final: 0.8700 (m) REVERT: A 710 GLU cc_start: 0.7872 (pt0) cc_final: 0.7524 (tt0) REVERT: B 508 GLN cc_start: 0.8576 (pt0) cc_final: 0.8354 (tp40) REVERT: B 587 GLN cc_start: 0.5167 (mm-40) cc_final: 0.4657 (mm-40) REVERT: B 613 ILE cc_start: 0.9493 (pt) cc_final: 0.9101 (mm) REVERT: B 759 LEU cc_start: 0.9466 (mt) cc_final: 0.9028 (tt) REVERT: C 397 VAL cc_start: 0.9341 (t) cc_final: 0.9069 (m) REVERT: C 528 CYS cc_start: 0.9312 (m) cc_final: 0.8908 (p) REVERT: C 545 ARG cc_start: 0.7102 (mmt180) cc_final: 0.6774 (mmt180) REVERT: C 585 MET cc_start: 0.6305 (mtt) cc_final: 0.5870 (mtt) REVERT: C 668 ASP cc_start: 0.9154 (t0) cc_final: 0.8621 (m-30) REVERT: C 674 MET cc_start: 0.8005 (ptm) cc_final: 0.7086 (ttm) REVERT: C 675 ARG cc_start: 0.9048 (ppt170) cc_final: 0.8691 (ptm160) REVERT: D 425 CYS cc_start: 0.8430 (m) cc_final: 0.7393 (p) REVERT: D 533 TYR cc_start: 0.6894 (t80) cc_final: 0.6585 (t80) REVERT: D 581 LEU cc_start: 0.8431 (tt) cc_final: 0.8167 (tp) REVERT: D 693 VAL cc_start: 0.9268 (t) cc_final: 0.8762 (p) REVERT: E 9 MET cc_start: 0.8591 (ppp) cc_final: 0.8364 (ppp) REVERT: E 140 PHE cc_start: 0.8422 (m-80) cc_final: 0.8145 (m-10) REVERT: E 199 MET cc_start: 0.8367 (mmp) cc_final: 0.7767 (mtp) REVERT: F 32 TRP cc_start: 0.7051 (m-10) cc_final: 0.6739 (m-10) REVERT: F 68 LEU cc_start: 0.8494 (pp) cc_final: 0.8182 (tp) REVERT: F 131 HIS cc_start: 0.7973 (m-70) cc_final: 0.7729 (m170) REVERT: G 9 MET cc_start: 0.8447 (mtm) cc_final: 0.8242 (mtt) REVERT: G 106 PHE cc_start: 0.8781 (m-80) cc_final: 0.8337 (m-80) REVERT: H 130 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6827 (mmp-170) REVERT: H 199 MET cc_start: 0.6073 (ttp) cc_final: 0.5590 (ttm) outliers start: 6 outliers final: 1 residues processed: 371 average time/residue: 0.1505 time to fit residues: 82.9423 Evaluate side-chains 269 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 1.9990 chunk 134 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS F 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094314 restraints weight = 54293.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094720 restraints weight = 46733.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095125 restraints weight = 35442.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095484 restraints weight = 32659.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095541 restraints weight = 31081.733| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18475 Z= 0.153 Angle : 0.646 7.986 24942 Z= 0.348 Chirality : 0.043 0.220 2799 Planarity : 0.005 0.067 3066 Dihedral : 6.332 85.869 2498 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2276 helix: 0.18 (0.15), residues: 1147 sheet: -1.19 (0.50), residues: 113 loop : -1.19 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 599 TYR 0.021 0.002 TYR A 523 PHE 0.043 0.002 PHE C 574 TRP 0.026 0.002 TRP D 578 HIS 0.008 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00321 (18463) covalent geometry : angle 0.64559 (24918) SS BOND : bond 0.00383 ( 12) SS BOND : angle 1.20838 ( 24) hydrogen bonds : bond 0.04646 ( 847) hydrogen bonds : angle 4.88749 ( 2397) *********************** 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 358 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.725 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: 0.8848 (m-80) cc_final: 0.8400 (m-80) REVERT: A 518 LEU cc_start: 0.9208 (mt) cc_final: 0.8572 (pp) REVERT: A 527 MET cc_start: 0.8287 (mmt) cc_final: 0.8005 (tpp) REVERT: A 681 VAL cc_start: 0.8888 (p) cc_final: 0.8673 (m) REVERT: B 414 MET cc_start: 0.7658 (mpp) cc_final: 0.6340 (ppp) REVERT: B 486 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 503 MET cc_start: 0.9280 (ppp) cc_final: 0.8911 (ppp) REVERT: B 508 GLN cc_start: 0.8505 (pt0) cc_final: 0.8204 (mm-40) REVERT: B 587 GLN cc_start: 0.5286 (mm-40) cc_final: 0.4406 (mm-40) REVERT: B 759 LEU cc_start: 0.9479 (mt) cc_final: 0.9088 (tt) REVERT: C 397 VAL cc_start: 0.9317 (t) cc_final: 0.9053 (m) REVERT: C 486 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8061 (mt-10) REVERT: C 528 CYS cc_start: 0.9312 (m) cc_final: 0.8750 (p) REVERT: C 573 ILE cc_start: 0.8057 (mt) cc_final: 0.7325 (mt) REVERT: C 674 MET cc_start: 0.7954 (ptm) cc_final: 0.7628 (ttp) REVERT: C 675 ARG cc_start: 0.9132 (ppt170) cc_final: 0.8871 (ptm160) REVERT: D 425 CYS cc_start: 0.8332 (m) cc_final: 0.7813 (p) REVERT: D 503 MET cc_start: 0.8914 (ppp) cc_final: 0.8609 (ppp) REVERT: D 533 TYR cc_start: 0.6654 (t80) cc_final: 0.6382 (t80) REVERT: D 581 LEU cc_start: 0.8208 (tt) cc_final: 0.7942 (tp) REVERT: E 9 MET cc_start: 0.8562 (ppp) cc_final: 0.8238 (ppp) REVERT: E 116 MET cc_start: 0.7214 (mmm) cc_final: 0.6961 (mtt) REVERT: E 140 PHE cc_start: 0.8434 (m-80) cc_final: 0.7663 (m-80) REVERT: E 146 LEU cc_start: 0.9199 (tp) cc_final: 0.8914 (tp) REVERT: E 191 MET cc_start: 0.8157 (tmm) cc_final: 0.7847 (tpp) REVERT: E 199 MET cc_start: 0.8345 (mmp) cc_final: 0.7660 (mtp) REVERT: F 68 LEU cc_start: 0.8432 (pp) cc_final: 0.8224 (tp) REVERT: F 101 ARG cc_start: 0.8481 (tpt170) cc_final: 0.8247 (tpt-90) REVERT: G 69 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.3157 (pm20) REVERT: G 106 PHE cc_start: 0.8694 (m-80) cc_final: 0.8210 (m-80) REVERT: G 148 ASN cc_start: 0.8915 (m-40) cc_final: 0.8510 (m-40) REVERT: H 187 ILE cc_start: 0.8421 (mm) cc_final: 0.8192 (pt) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1443 time to fit residues: 77.6138 Evaluate side-chains 260 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 42 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 104 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN C 587 GLN D 412 HIS E 204 HIS ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095724 restraints weight = 55201.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095505 restraints weight = 47233.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096360 restraints weight = 39486.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096639 restraints weight = 33638.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096732 restraints weight = 31443.549| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3778 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= 0.143 Angle : 0.637 10.675 24942 Z= 0.338 Chirality : 0.042 0.248 2799 Planarity : 0.004 0.051 3066 Dihedral : 5.960 82.968 2498 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2276 helix: 0.32 (0.15), residues: 1148 sheet: -1.27 (0.47), residues: 128 loop : -1.18 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 599 TYR 0.022 0.001 TYR F 127 PHE 0.034 0.002 PHE A 574 TRP 0.039 0.002 TRP D 578 HIS 0.007 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00312 (18463) covalent geometry : angle 0.63647 (24918) SS BOND : bond 0.00337 ( 12) SS BOND : angle 1.04234 ( 24) hydrogen bonds : bond 0.04333 ( 847) hydrogen bonds : angle 4.69025 ( 2397) *********************** 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 332 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.707 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: A 491 PHE cc_start: 0.8869 (m-80) cc_final: 0.8473 (m-10) REVERT: A 508 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 518 LEU cc_start: 0.9234 (mt) cc_final: 0.8610 (pp) REVERT: A 527 MET cc_start: 0.8222 (mmt) cc_final: 0.7512 (tpp) REVERT: A 681 VAL cc_start: 0.8896 (p) cc_final: 0.8676 (m) REVERT: B 503 MET cc_start: 0.9237 (ppp) cc_final: 0.8847 (ppp) REVERT: B 508 GLN cc_start: 0.8418 (pt0) cc_final: 0.8128 (mm-40) REVERT: B 587 GLN cc_start: 0.5354 (mm-40) cc_final: 0.4470 (mm-40) REVERT: B 759 LEU cc_start: 0.9468 (mt) cc_final: 0.9106 (tt) REVERT: C 397 VAL cc_start: 0.9290 (t) cc_final: 0.8974 (m) REVERT: C 508 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8383 (tp-100) REVERT: C 528 CYS cc_start: 0.9251 (m) cc_final: 0.8735 (p) REVERT: C 573 ILE cc_start: 0.7932 (mt) cc_final: 0.7586 (mt) REVERT: C 604 VAL cc_start: 0.8574 (t) cc_final: 0.8272 (t) REVERT: C 811 LEU cc_start: 0.8423 (tt) cc_final: 0.8089 (mt) REVERT: D 425 CYS cc_start: 0.8407 (m) cc_final: 0.7742 (p) REVERT: D 463 MET cc_start: 0.9147 (mpp) cc_final: 0.8542 (mpp) REVERT: D 527 MET cc_start: 0.6617 (mmt) cc_final: 0.6384 (mmt) REVERT: D 533 TYR cc_start: 0.6635 (t80) cc_final: 0.6289 (t80) REVERT: D 581 LEU cc_start: 0.8228 (tt) cc_final: 0.7801 (tp) REVERT: D 813 GLU cc_start: 0.8360 (tt0) cc_final: 0.7697 (tp30) REVERT: E 9 MET cc_start: 0.8548 (ppp) cc_final: 0.8186 (ppp) REVERT: E 116 MET cc_start: 0.7141 (mmm) cc_final: 0.6924 (mtt) REVERT: E 140 PHE cc_start: 0.8387 (m-80) cc_final: 0.7669 (m-80) REVERT: E 146 LEU cc_start: 0.9193 (tp) cc_final: 0.8956 (tp) REVERT: E 199 MET cc_start: 0.8283 (mmp) cc_final: 0.7633 (mtp) REVERT: F 29 THR cc_start: 0.9334 (p) cc_final: 0.8921 (t) REVERT: G 9 MET cc_start: 0.8180 (mtm) cc_final: 0.7821 (mtt) REVERT: G 106 PHE cc_start: 0.8660 (m-80) cc_final: 0.8239 (m-80) REVERT: G 148 ASN cc_start: 0.8880 (m-40) cc_final: 0.8488 (m-40) REVERT: G 192 VAL cc_start: 0.9395 (p) cc_final: 0.9154 (p) REVERT: G 199 MET cc_start: 0.8869 (mtt) cc_final: 0.8063 (mmm) outliers start: 1 outliers final: 1 residues processed: 331 average time/residue: 0.1451 time to fit residues: 72.4354 Evaluate side-chains 255 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 53 optimal weight: 0.4980 chunk 149 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094536 restraints weight = 55220.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094924 restraints weight = 45664.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095067 restraints weight = 36063.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095351 restraints weight = 35498.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095489 restraints weight = 32972.104| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18475 Z= 0.148 Angle : 0.627 9.421 24942 Z= 0.334 Chirality : 0.042 0.192 2799 Planarity : 0.004 0.047 3066 Dihedral : 5.729 80.213 2498 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2276 helix: 0.39 (0.15), residues: 1167 sheet: -1.54 (0.48), residues: 120 loop : -1.26 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 599 TYR 0.014 0.001 TYR A 523 PHE 0.036 0.002 PHE A 574 TRP 0.061 0.002 TRP C 606 HIS 0.004 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00327 (18463) covalent geometry : angle 0.62624 (24918) SS BOND : bond 0.00299 ( 12) SS BOND : angle 1.34863 ( 24) hydrogen bonds : bond 0.04188 ( 847) hydrogen bonds : angle 4.61803 ( 2397) *********************** 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 323 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.722 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: 0.8904 (m-80) cc_final: 0.8630 (m-10) REVERT: A 518 LEU cc_start: 0.9235 (mt) cc_final: 0.8598 (pp) REVERT: A 527 MET cc_start: 0.8198 (mmt) cc_final: 0.7854 (tpp) REVERT: B 503 MET cc_start: 0.9235 (ppp) cc_final: 0.8789 (ppp) REVERT: B 508 GLN cc_start: 0.8546 (pt0) cc_final: 0.8122 (mm-40) REVERT: B 587 GLN cc_start: 0.5432 (mm-40) cc_final: 0.5198 (mp10) REVERT: B 759 LEU cc_start: 0.9469 (mt) cc_final: 0.9128 (tt) REVERT: C 397 VAL cc_start: 0.9317 (t) cc_final: 0.8951 (m) REVERT: C 508 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8398 (tp-100) REVERT: C 528 CYS cc_start: 0.9348 (m) cc_final: 0.9129 (m) REVERT: C 573 ILE cc_start: 0.8004 (mt) cc_final: 0.7653 (mt) REVERT: C 811 LEU cc_start: 0.8501 (tt) cc_final: 0.8168 (mt) REVERT: D 527 MET cc_start: 0.6881 (mmt) cc_final: 0.6472 (mmt) REVERT: D 813 GLU cc_start: 0.8362 (tt0) cc_final: 0.7740 (tp30) REVERT: E 9 MET cc_start: 0.8511 (ppp) cc_final: 0.8174 (ppp) REVERT: E 116 MET cc_start: 0.7212 (mmm) cc_final: 0.6849 (mtt) REVERT: E 140 PHE cc_start: 0.8475 (m-80) cc_final: 0.7746 (m-80) REVERT: E 146 LEU cc_start: 0.9233 (tp) cc_final: 0.9027 (tp) REVERT: E 188 ILE cc_start: 0.8517 (tp) cc_final: 0.7765 (tp) REVERT: E 190 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8643 (mp0) REVERT: E 199 MET cc_start: 0.8344 (mmp) cc_final: 0.7757 (ttm) REVERT: F 29 THR cc_start: 0.9332 (p) cc_final: 0.9112 (t) REVERT: G 9 MET cc_start: 0.8349 (mtm) cc_final: 0.7961 (mtt) REVERT: G 101 ARG cc_start: 0.9063 (tpt170) cc_final: 0.8763 (tpt90) REVERT: G 106 PHE cc_start: 0.8666 (m-80) cc_final: 0.8270 (m-10) REVERT: G 148 ASN cc_start: 0.8908 (m-40) cc_final: 0.8511 (m-40) REVERT: G 195 LEU cc_start: 0.9391 (mt) cc_final: 0.9174 (mt) REVERT: G 199 MET cc_start: 0.9038 (mtt) cc_final: 0.8161 (mmm) REVERT: H 23 MET cc_start: 0.5089 (tpp) cc_final: 0.4873 (tpp) REVERT: H 191 MET cc_start: 0.7566 (mmp) cc_final: 0.7359 (mmm) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1467 time to fit residues: 71.3153 Evaluate side-chains 258 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** D 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094248 restraints weight = 54536.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093926 restraints weight = 55290.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094080 restraints weight = 44671.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094639 restraints weight = 39716.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095000 restraints weight = 34026.567| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18475 Z= 0.155 Angle : 0.636 12.443 24942 Z= 0.335 Chirality : 0.042 0.237 2799 Planarity : 0.004 0.047 3066 Dihedral : 5.554 77.001 2498 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2276 helix: 0.52 (0.15), residues: 1165 sheet: -1.49 (0.46), residues: 131 loop : -1.23 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 453 TYR 0.014 0.001 TYR C 702 PHE 0.029 0.002 PHE A 574 TRP 0.032 0.002 TRP E 32 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00340 (18463) covalent geometry : angle 0.63520 (24918) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.27728 ( 24) hydrogen bonds : bond 0.04200 ( 847) hydrogen bonds : angle 4.59279 ( 2397) *********************** 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 318 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.761 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 431 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7611 (tp30) REVERT: A 491 PHE cc_start: 0.8927 (m-80) cc_final: 0.8628 (m-10) REVERT: A 518 LEU cc_start: 0.9247 (mt) cc_final: 0.8549 (pp) REVERT: A 527 MET cc_start: 0.8346 (mmt) cc_final: 0.7906 (tpp) REVERT: B 503 MET cc_start: 0.9249 (ppp) cc_final: 0.8906 (ppp) REVERT: B 508 GLN cc_start: 0.8480 (pt0) cc_final: 0.8073 (mm-40) REVERT: B 587 GLN cc_start: 0.5658 (mm-40) cc_final: 0.5343 (mp10) REVERT: B 759 LEU cc_start: 0.9444 (mt) cc_final: 0.9105 (tt) REVERT: C 397 VAL cc_start: 0.9429 (t) cc_final: 0.9081 (m) REVERT: C 508 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8402 (tp-100) REVERT: C 670 MET cc_start: 0.9218 (ptm) cc_final: 0.9000 (ptp) REVERT: C 674 MET cc_start: 0.8513 (ptp) cc_final: 0.7746 (ttp) REVERT: C 811 LEU cc_start: 0.8469 (tt) cc_final: 0.8174 (mt) REVERT: D 425 CYS cc_start: 0.8315 (m) cc_final: 0.7712 (p) REVERT: D 527 MET cc_start: 0.7196 (mmt) cc_final: 0.6599 (mmt) REVERT: D 581 LEU cc_start: 0.8425 (tt) cc_final: 0.8180 (tp) REVERT: E 9 MET cc_start: 0.8527 (ppp) cc_final: 0.8161 (ppp) REVERT: E 116 MET cc_start: 0.7173 (mmm) cc_final: 0.6669 (mtt) REVERT: E 140 PHE cc_start: 0.8373 (m-80) cc_final: 0.7792 (m-80) REVERT: E 146 LEU cc_start: 0.9267 (tp) cc_final: 0.9015 (tp) REVERT: E 199 MET cc_start: 0.8258 (mmp) cc_final: 0.7739 (ttm) REVERT: F 101 ARG cc_start: 0.8517 (tpt-90) cc_final: 0.8235 (tpt-90) REVERT: G 9 MET cc_start: 0.8316 (mtm) cc_final: 0.8003 (mtt) REVERT: G 101 ARG cc_start: 0.8980 (tpt170) cc_final: 0.8732 (tpt90) REVERT: G 148 ASN cc_start: 0.8879 (m-40) cc_final: 0.8529 (m-40) REVERT: G 192 VAL cc_start: 0.8909 (t) cc_final: 0.8695 (t) REVERT: G 199 MET cc_start: 0.8884 (mtt) cc_final: 0.8072 (mmm) REVERT: H 191 MET cc_start: 0.7641 (mmp) cc_final: 0.7369 (mmm) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1416 time to fit residues: 67.7615 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 : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 205 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 146 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 159 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095758 restraints weight = 55077.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095505 restraints weight = 50939.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095808 restraints weight = 41086.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096131 restraints weight = 36896.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096326 restraints weight = 34776.296| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4526 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= 0.129 Angle : 0.611 10.886 24942 Z= 0.319 Chirality : 0.041 0.193 2799 Planarity : 0.004 0.045 3066 Dihedral : 5.303 72.793 2498 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2276 helix: 0.64 (0.15), residues: 1172 sheet: -1.30 (0.49), residues: 121 loop : -1.14 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 36 TYR 0.015 0.001 TYR D 533 PHE 0.028 0.001 PHE A 531 TRP 0.070 0.002 TRP C 606 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00278 (18463) covalent geometry : angle 0.61111 (24918) SS BOND : bond 0.00310 ( 12) SS BOND : angle 0.92505 ( 24) hydrogen bonds : bond 0.03868 ( 847) hydrogen bonds : angle 4.44962 ( 2397) *********************** 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 325 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.545 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: 0.7765 (mm-30) cc_final: 0.7462 (tp30) REVERT: A 491 PHE cc_start: 0.8935 (m-80) cc_final: 0.8634 (m-10) REVERT: A 518 LEU cc_start: 0.9231 (mt) cc_final: 0.8624 (pp) REVERT: B 503 MET cc_start: 0.9232 (ppp) cc_final: 0.8942 (ppp) REVERT: B 508 GLN cc_start: 0.8422 (pt0) cc_final: 0.8023 (mm-40) REVERT: B 670 MET cc_start: 0.8164 (mmp) cc_final: 0.7912 (mmp) REVERT: C 397 VAL cc_start: 0.9445 (t) cc_final: 0.9105 (m) REVERT: C 573 ILE cc_start: 0.7948 (mt) cc_final: 0.7692 (mt) REVERT: C 670 MET cc_start: 0.9182 (ptm) cc_final: 0.8872 (ptp) REVERT: C 674 MET cc_start: 0.8459 (ptp) cc_final: 0.7563 (ttp) REVERT: C 811 LEU cc_start: 0.8479 (tt) cc_final: 0.8191 (mt) REVERT: D 399 THR cc_start: 0.7694 (t) cc_final: 0.7471 (t) REVERT: D 425 CYS cc_start: 0.8442 (m) cc_final: 0.7718 (p) REVERT: D 527 MET cc_start: 0.7210 (mmt) cc_final: 0.6578 (mmt) REVERT: D 533 TYR cc_start: 0.6842 (t80) cc_final: 0.6461 (t80) REVERT: D 578 TRP cc_start: 0.7316 (t-100) cc_final: 0.7058 (t60) REVERT: D 581 LEU cc_start: 0.8553 (tt) cc_final: 0.7948 (tp) REVERT: D 813 GLU cc_start: 0.8353 (tt0) cc_final: 0.7690 (tp30) REVERT: E 9 MET cc_start: 0.8403 (ppp) cc_final: 0.7980 (ppp) REVERT: E 116 MET cc_start: 0.7144 (mmm) cc_final: 0.6675 (mtt) REVERT: E 140 PHE cc_start: 0.8363 (m-80) cc_final: 0.7892 (m-80) REVERT: E 188 ILE cc_start: 0.8599 (tt) cc_final: 0.8334 (tt) REVERT: E 199 MET cc_start: 0.8269 (mmp) cc_final: 0.7726 (mtp) REVERT: G 9 MET cc_start: 0.8322 (mtm) cc_final: 0.8017 (mtt) REVERT: G 77 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8895 (ptmt) REVERT: G 106 PHE cc_start: 0.8644 (m-80) cc_final: 0.8370 (m-10) REVERT: G 148 ASN cc_start: 0.8854 (m-40) cc_final: 0.8508 (m-40) REVERT: G 195 LEU cc_start: 0.9370 (mt) cc_final: 0.9163 (mt) REVERT: G 199 MET cc_start: 0.8884 (mtt) cc_final: 0.8071 (mmm) REVERT: H 59 HIS cc_start: 0.3157 (p90) cc_final: 0.2554 (p90) REVERT: H 130 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6524 (mmp-170) REVERT: H 191 MET cc_start: 0.7602 (mmp) cc_final: 0.7357 (mmm) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1414 time to fit residues: 70.0266 Evaluate side-chains 248 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 29 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 0.0770 chunk 171 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN F 148 ASN ** F 159 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.116833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092717 restraints weight = 56267.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.092334 restraints weight = 50329.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092480 restraints weight = 43097.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092802 restraints weight = 38920.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093007 restraints weight = 35865.108| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18475 Z= 0.220 Angle : 0.716 16.156 24942 Z= 0.373 Chirality : 0.044 0.198 2799 Planarity : 0.005 0.043 3066 Dihedral : 5.571 69.313 2498 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.27 % Favored : 94.55 % Rotamer: Outliers : 0.05 % Allowed : 1.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2276 helix: 0.48 (0.15), residues: 1165 sheet: -1.48 (0.49), residues: 121 loop : -1.34 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 101 TYR 0.021 0.002 TYR A 523 PHE 0.027 0.002 PHE A 574 TRP 0.076 0.003 TRP C 606 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00493 (18463) covalent geometry : angle 0.71536 (24918) SS BOND : bond 0.00244 ( 12) SS BOND : angle 0.90486 ( 24) hydrogen bonds : bond 0.04423 ( 847) hydrogen bonds : angle 4.84567 ( 2397) *********************** 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 296 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.739 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: 0.9014 (m-80) cc_final: 0.8729 (m-10) REVERT: A 518 LEU cc_start: 0.9210 (mt) cc_final: 0.8628 (pp) REVERT: A 527 MET cc_start: 0.8551 (tpp) cc_final: 0.8248 (tpp) REVERT: B 503 MET cc_start: 0.9340 (ppp) cc_final: 0.9004 (ppp) REVERT: B 508 GLN cc_start: 0.8347 (pt0) cc_final: 0.8036 (mm-40) REVERT: C 573 ILE cc_start: 0.7885 (mt) cc_final: 0.7604 (mt) REVERT: C 670 MET cc_start: 0.9197 (ptm) cc_final: 0.8972 (ptp) REVERT: C 674 MET cc_start: 0.8613 (ptp) cc_final: 0.7652 (ttp) REVERT: C 811 LEU cc_start: 0.8505 (tt) cc_final: 0.8192 (mt) REVERT: D 533 TYR cc_start: 0.6928 (t80) cc_final: 0.6724 (t80) REVERT: D 581 LEU cc_start: 0.8566 (tt) cc_final: 0.8219 (tp) REVERT: D 769 ASP cc_start: 0.8820 (m-30) cc_final: 0.8616 (m-30) REVERT: D 813 GLU cc_start: 0.8379 (tt0) cc_final: 0.7782 (tp30) REVERT: E 9 MET cc_start: 0.8503 (ppp) cc_final: 0.7687 (ppp) REVERT: E 116 MET cc_start: 0.7222 (mmm) cc_final: 0.6571 (mtt) REVERT: E 140 PHE cc_start: 0.8438 (m-80) cc_final: 0.7858 (m-80) REVERT: E 188 ILE cc_start: 0.8673 (tt) cc_final: 0.8380 (tt) REVERT: E 199 MET cc_start: 0.8261 (mmp) cc_final: 0.7541 (mmt) REVERT: F 32 TRP cc_start: 0.6686 (m-10) cc_final: 0.6194 (m-10) REVERT: F 101 ARG cc_start: 0.8537 (tpt-90) cc_final: 0.8205 (tpt-90) REVERT: G 9 MET cc_start: 0.8343 (mtm) cc_final: 0.8013 (mtt) REVERT: G 148 ASN cc_start: 0.8927 (m-40) cc_final: 0.8566 (m-40) REVERT: G 199 MET cc_start: 0.8925 (mtt) cc_final: 0.8133 (mmm) REVERT: H 130 ARG cc_start: 0.6765 (mtt180) cc_final: 0.6553 (mmp-170) REVERT: H 131 HIS cc_start: 0.7902 (m-70) cc_final: 0.7690 (m-70) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.1216 time to fit residues: 55.3441 Evaluate side-chains 242 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093568 restraints weight = 54851.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093812 restraints weight = 45808.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093930 restraints weight = 37707.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094253 restraints weight = 36033.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094511 restraints weight = 33102.270| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4872 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= 0.150 Angle : 0.657 10.787 24942 Z= 0.341 Chirality : 0.042 0.174 2799 Planarity : 0.004 0.045 3066 Dihedral : 5.358 65.339 2498 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.18), residues: 2276 helix: 0.58 (0.15), residues: 1170 sheet: -1.42 (0.50), residues: 121 loop : -1.22 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 101 TYR 0.019 0.001 TYR A 523 PHE 0.027 0.001 PHE A 574 TRP 0.071 0.003 TRP C 606 HIS 0.003 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00333 (18463) covalent geometry : angle 0.65725 (24918) SS BOND : bond 0.00271 ( 12) SS BOND : angle 0.78076 ( 24) hydrogen bonds : bond 0.04127 ( 847) hydrogen bonds : angle 4.62154 ( 2397) *********************** 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 312 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.424 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 491 PHE cc_start: 0.8961 (m-80) cc_final: 0.8566 (m-10) REVERT: A 518 LEU cc_start: 0.9215 (mt) cc_final: 0.8648 (pp) REVERT: A 527 MET cc_start: 0.8384 (tpp) cc_final: 0.7757 (mpp) REVERT: A 623 PHE cc_start: 0.8560 (m-10) cc_final: 0.8332 (m-80) REVERT: B 503 MET cc_start: 0.9233 (ppp) cc_final: 0.8954 (ppp) REVERT: B 508 GLN cc_start: 0.8252 (pt0) cc_final: 0.7930 (mm-40) REVERT: B 670 MET cc_start: 0.8229 (mmp) cc_final: 0.8023 (mmp) REVERT: C 432 ILE cc_start: 0.9498 (mm) cc_final: 0.9290 (mm) REVERT: C 508 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8288 (tp-100) REVERT: C 668 ASP cc_start: 0.9148 (t70) cc_final: 0.8530 (m-30) REVERT: C 811 LEU cc_start: 0.8468 (tt) cc_final: 0.8142 (mt) REVERT: D 533 TYR cc_start: 0.6935 (t80) cc_final: 0.6506 (t80) REVERT: D 581 LEU cc_start: 0.8554 (tt) cc_final: 0.7973 (tp) REVERT: D 769 ASP cc_start: 0.8858 (m-30) cc_final: 0.8597 (m-30) REVERT: D 813 GLU cc_start: 0.8411 (tt0) cc_final: 0.7767 (tp30) REVERT: E 9 MET cc_start: 0.8393 (ppp) cc_final: 0.7882 (ppp) REVERT: E 116 MET cc_start: 0.7197 (mmm) cc_final: 0.6582 (mtt) REVERT: E 140 PHE cc_start: 0.8472 (m-80) cc_final: 0.7993 (m-80) REVERT: E 188 ILE cc_start: 0.8610 (tt) cc_final: 0.8369 (tt) REVERT: E 190 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8361 (mp0) REVERT: E 199 MET cc_start: 0.8258 (mmp) cc_final: 0.7620 (ttm) REVERT: F 32 TRP cc_start: 0.6577 (m-10) cc_final: 0.6081 (m-10) REVERT: G 9 MET cc_start: 0.8325 (mtm) cc_final: 0.7970 (mtt) REVERT: G 77 LYS cc_start: 0.9155 (ptmt) cc_final: 0.8936 (ptmt) REVERT: G 98 ARG cc_start: 0.8874 (ptp-170) cc_final: 0.8635 (ptt-90) REVERT: G 148 ASN cc_start: 0.8887 (m-40) cc_final: 0.8583 (m-40) REVERT: G 192 VAL cc_start: 0.8984 (t) cc_final: 0.8695 (t) REVERT: G 195 LEU cc_start: 0.9368 (mt) cc_final: 0.9137 (mt) REVERT: G 199 MET cc_start: 0.8950 (mtt) cc_final: 0.8094 (mmm) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1224 time to fit residues: 57.9729 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 : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 213 optimal weight: 8.9990 chunk 83 optimal weight: 0.0070 chunk 67 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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** F 148 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095917 restraints weight = 54680.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095926 restraints weight = 47571.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097043 restraints weight = 38469.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097085 restraints weight = 30058.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097251 restraints weight = 29868.813| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5029 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= 0.123 Angle : 0.639 11.286 24942 Z= 0.329 Chirality : 0.042 0.173 2799 Planarity : 0.004 0.047 3066 Dihedral : 5.058 60.298 2498 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2276 helix: 0.61 (0.15), residues: 1176 sheet: -1.66 (0.47), residues: 130 loop : -1.14 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 98 TYR 0.017 0.001 TYR A 523 PHE 0.030 0.001 PHE A 541 TRP 0.068 0.003 TRP C 606 HIS 0.003 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00261 (18463) covalent geometry : angle 0.63929 (24918) SS BOND : bond 0.00230 ( 12) SS BOND : angle 0.70158 ( 24) hydrogen bonds : bond 0.03872 ( 847) hydrogen bonds : angle 4.46988 ( 2397) ********************** 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 312 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.696 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: A 491 PHE cc_start: 0.8873 (m-80) cc_final: 0.8443 (m-10) REVERT: A 518 LEU cc_start: 0.9217 (mt) cc_final: 0.8612 (pp) REVERT: A 527 MET cc_start: 0.8330 (tpp) cc_final: 0.7688 (mpp) REVERT: B 414 MET cc_start: 0.7660 (pmm) cc_final: 0.7404 (pmm) REVERT: B 503 MET cc_start: 0.9213 (ppp) cc_final: 0.8822 (ppp) REVERT: B 508 GLN cc_start: 0.8110 (pt0) cc_final: 0.7816 (mm-40) REVERT: B 670 MET cc_start: 0.8218 (mmp) cc_final: 0.8003 (mmp) REVERT: C 508 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8363 (tp-100) REVERT: C 668 ASP cc_start: 0.9102 (t70) cc_final: 0.8493 (m-30) REVERT: C 670 MET cc_start: 0.9326 (ptp) cc_final: 0.9122 (ptp) REVERT: C 688 GLU cc_start: 0.8654 (pt0) cc_final: 0.8405 (pt0) REVERT: C 811 LEU cc_start: 0.8408 (tt) cc_final: 0.8152 (mt) REVERT: D 533 TYR cc_start: 0.6857 (t80) cc_final: 0.6411 (t80) REVERT: D 578 TRP cc_start: 0.7295 (t-100) cc_final: 0.7073 (t60) REVERT: D 581 LEU cc_start: 0.8470 (tt) cc_final: 0.7799 (tp) REVERT: D 769 ASP cc_start: 0.8830 (m-30) cc_final: 0.8557 (m-30) REVERT: D 813 GLU cc_start: 0.8304 (tt0) cc_final: 0.7716 (tp30) REVERT: E 9 MET cc_start: 0.8394 (ppp) cc_final: 0.7893 (ppp) REVERT: E 106 PHE cc_start: 0.8682 (m-80) cc_final: 0.8391 (m-80) REVERT: E 116 MET cc_start: 0.7215 (mmm) cc_final: 0.6464 (mtt) REVERT: E 140 PHE cc_start: 0.8322 (m-80) cc_final: 0.7727 (m-80) REVERT: E 188 ILE cc_start: 0.8607 (tt) cc_final: 0.8297 (tt) REVERT: E 190 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8400 (mp0) REVERT: E 199 MET cc_start: 0.8157 (mmp) cc_final: 0.7588 (ttm) REVERT: F 32 TRP cc_start: 0.6648 (m-10) cc_final: 0.6125 (m-10) REVERT: F 101 ARG cc_start: 0.8456 (tpt-90) cc_final: 0.8245 (tpt-90) REVERT: G 9 MET cc_start: 0.8331 (mtm) cc_final: 0.8040 (mtt) REVERT: G 98 ARG cc_start: 0.8784 (ptp-170) cc_final: 0.8573 (ptt-90) REVERT: G 106 PHE cc_start: 0.8649 (m-80) cc_final: 0.8414 (m-10) REVERT: G 148 ASN cc_start: 0.8883 (m-40) cc_final: 0.8518 (m-40) REVERT: G 199 MET cc_start: 0.8802 (mtt) cc_final: 0.8036 (mmm) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1211 time to fit residues: 57.4862 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 147 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 229 optimal weight: 0.3980 chunk 152 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** F 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096017 restraints weight = 54830.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096277 restraints weight = 47763.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096442 restraints weight = 37829.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096821 restraints weight = 36451.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096887 restraints weight = 34134.986| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18475 Z= 0.125 Angle : 0.639 11.946 24942 Z= 0.329 Chirality : 0.042 0.152 2799 Planarity : 0.004 0.069 3066 Dihedral : 4.938 55.748 2498 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2276 helix: 0.68 (0.16), residues: 1171 sheet: -1.92 (0.45), residues: 126 loop : -1.20 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 101 TYR 0.017 0.001 TYR A 523 PHE 0.028 0.001 PHE A 574 TRP 0.062 0.002 TRP C 606 HIS 0.003 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00271 (18463) covalent geometry : angle 0.63800 (24918) SS BOND : bond 0.00478 ( 12) SS BOND : angle 1.30217 ( 24) hydrogen bonds : bond 0.03831 ( 847) hydrogen bonds : angle 4.54862 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.38 seconds wall clock time: 49 minutes 48.14 seconds (2988.14 seconds total)