Starting phenix.real_space_refine on Wed Sep 25 07:32:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/09_2024/8k3t_36859.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 6178 2.51 5 N 1482 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.04, per 1000 atoms: 0.64 Number of scatterers: 9410 At special positions: 0 Unit cell: (113.42, 109.18, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 4 11.99 O 1682 8.00 N 1482 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 67.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.876A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 516 removed outlier: 4.155A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.617A pdb=" N ARG A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.817A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.539A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.748A pdb=" N GLY A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.627A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.602A pdb=" N TRP A 779 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 933 Processing helix chain 'A' and resid 942 through 955 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1130 removed outlier: 4.073A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.875A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.154A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.615A pdb=" N ARG B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.818A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.540A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.749A pdb=" N GLY B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.626A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.603A pdb=" N TRP B 779 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 933 Processing helix chain 'B' and resid 942 through 955 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1130 removed outlier: 4.071A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.683A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.770A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.682A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 4.769A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.45: 2673 1.45 - 1.57: 5244 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 9642 Sorted by residual: bond pdb=" O1A UDP B1502 " pdb=" PA UDP B1502 " ideal model delta sigma weight residual 1.482 1.527 -0.045 1.00e-02 1.00e+04 1.99e+01 bond pdb=" O1A UDP A1502 " pdb=" PA UDP A1502 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" N ILE A 493 " pdb=" CA ILE A 493 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 533 " pdb=" CA VAL B 533 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.15e-02 7.56e+03 9.53e+00 bond pdb=" N ILE B 493 " pdb=" CA ILE B 493 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.37e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12580 2.05 - 4.09: 515 4.09 - 6.14: 57 6.14 - 8.18: 16 8.18 - 10.23: 4 Bond angle restraints: 13172 Sorted by residual: angle pdb=" CA PHE B 831 " pdb=" C PHE B 831 " pdb=" N ASN B 832 " ideal model delta sigma weight residual 118.27 108.41 9.86 1.59e+00 3.96e-01 3.84e+01 angle pdb=" CA PHE A 831 " pdb=" C PHE A 831 " pdb=" N ASN A 832 " ideal model delta sigma weight residual 118.27 108.42 9.85 1.59e+00 3.96e-01 3.84e+01 angle pdb=" O5' UDP A1502 " pdb=" PA UDP A1502 " pdb=" O1A UDP A1502 " ideal model delta sigma weight residual 106.70 111.20 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" O5' UDP B1502 " pdb=" PA UDP B1502 " pdb=" O1A UDP B1502 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" O2A UDP B1502 " pdb=" PA UDP B1502 " pdb=" O3A UDP B1502 " ideal model delta sigma weight residual 105.97 110.25 -4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 13167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 5282 23.20 - 46.40: 230 46.40 - 69.59: 42 69.59 - 92.79: 24 92.79 - 115.99: 2 Dihedral angle restraints: 5580 sinusoidal: 1878 harmonic: 3702 Sorted by residual: dihedral pdb=" C27 POV B1503 " pdb=" C28 POV B1503 " pdb=" C29 POV B1503 " pdb="C210 POV B1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.53 -115.99 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C27 POV A1503 " pdb=" C28 POV A1503 " pdb=" C29 POV A1503 " pdb="C210 POV A1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.59 -115.93 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA PHE A 911 " pdb=" C PHE A 911 " pdb=" N ARG A 912 " pdb=" CA ARG A 912 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 939 0.041 - 0.082: 444 0.082 - 0.124: 128 0.124 - 0.165: 29 0.165 - 0.206: 10 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA ILE B 719 " pdb=" N ILE B 719 " pdb=" C ILE B 719 " pdb=" CB ILE B 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL A 421 " pdb=" N VAL A 421 " pdb=" C VAL A 421 " pdb=" CB VAL A 421 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1547 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1503 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C29 POV A1503 " 0.059 2.00e-02 2.50e+03 pdb="C210 POV A1503 " -0.059 2.00e-02 2.50e+03 pdb="C211 POV A1503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1503 " 0.025 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C29 POV B1503 " -0.059 2.00e-02 2.50e+03 pdb="C210 POV B1503 " 0.059 2.00e-02 2.50e+03 pdb="C211 POV B1503 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 606 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 607 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.026 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1967 2.76 - 3.30: 10068 3.30 - 3.83: 15870 3.83 - 4.36: 17632 4.36 - 4.90: 29939 Nonbonded interactions: 75476 Sorted by model distance: nonbonded pdb=" O ALA A 511 " pdb=" OG SER A 515 " model vdw 2.225 3.040 nonbonded pdb=" O ALA B 511 " pdb=" OG SER B 515 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU A1060 " pdb=" OG1 THR A1091 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B1060 " pdb=" OG1 THR B1091 " model vdw 2.263 3.040 nonbonded pdb=" O1A UDP B1502 " pdb="MG MG B1504 " model vdw 2.287 2.170 ... (remaining 75471 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' selection = chain 'B' } 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: 0.460 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.070 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 9642 Z= 0.605 Angle : 0.929 10.229 13172 Z= 0.555 Chirality : 0.052 0.206 1550 Planarity : 0.005 0.047 1612 Dihedral : 15.004 115.988 3184 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.12 % Allowed : 1.34 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1234 helix: 1.11 (0.20), residues: 672 sheet: -0.96 (0.44), residues: 154 loop : -0.47 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 806 HIS 0.006 0.002 HIS B 783 PHE 0.021 0.002 PHE A1052 TYR 0.028 0.002 TYR B 878 ARG 0.004 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2570 (p0) REVERT: A 437 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8097 (mm110) REVERT: A 560 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8429 (tp40) REVERT: A 568 LEU cc_start: 0.7665 (tt) cc_final: 0.7193 (mp) REVERT: A 823 ILE cc_start: 0.9063 (tt) cc_final: 0.8791 (tt) REVERT: A 886 MET cc_start: 0.8323 (mtt) cc_final: 0.7679 (tmm) REVERT: B 411 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2657 (p0) REVERT: B 437 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 560 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8454 (tp40) REVERT: B 568 LEU cc_start: 0.7621 (tt) cc_final: 0.7191 (mp) REVERT: B 823 ILE cc_start: 0.9066 (tt) cc_final: 0.8786 (tt) REVERT: B 886 MET cc_start: 0.8316 (mtt) cc_final: 0.7693 (tmm) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 0.1758 time to fit residues: 40.5976 Evaluate side-chains 111 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 411 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9642 Z= 0.178 Angle : 0.557 7.063 13172 Z= 0.300 Chirality : 0.041 0.157 1550 Planarity : 0.003 0.037 1612 Dihedral : 12.668 118.092 1474 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.89 % Allowed : 6.49 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1234 helix: 1.83 (0.19), residues: 742 sheet: -0.48 (0.45), residues: 152 loop : -0.59 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1103 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE B 864 TYR 0.016 0.002 TYR A 713 ARG 0.003 0.000 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 0.937 Fit side-chains REVERT: A 560 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8418 (tp40) REVERT: A 879 MET cc_start: 0.8456 (ttp) cc_final: 0.8175 (ttp) REVERT: A 938 MET cc_start: 0.8608 (tpp) cc_final: 0.8372 (tpp) REVERT: B 543 MET cc_start: 0.6866 (pmm) cc_final: 0.6535 (ptp) REVERT: B 560 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8444 (tp40) REVERT: B 568 LEU cc_start: 0.7592 (tt) cc_final: 0.7202 (mp) REVERT: B 879 MET cc_start: 0.8451 (ttp) cc_final: 0.8171 (ttp) REVERT: B 938 MET cc_start: 0.8613 (tpp) cc_final: 0.8354 (tpp) outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.1521 time to fit residues: 34.0569 Evaluate side-chains 110 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS A 774 HIS B 582 HIS B 774 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9642 Z= 0.262 Angle : 0.550 5.966 13172 Z= 0.294 Chirality : 0.041 0.170 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.881 131.324 1470 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.68 % Allowed : 11.19 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1234 helix: 2.01 (0.19), residues: 754 sheet: -0.37 (0.45), residues: 152 loop : -0.59 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 PHE 0.025 0.002 PHE B 772 TYR 0.012 0.002 TYR A 713 ARG 0.004 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 459 HIS cc_start: 0.7501 (p-80) cc_final: 0.6719 (p-80) REVERT: A 543 MET cc_start: 0.6998 (pmm) cc_final: 0.6598 (ptp) REVERT: A 560 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8429 (tp40) REVERT: A 938 MET cc_start: 0.8695 (tpp) cc_final: 0.8393 (tpp) REVERT: A 1066 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8257 (t70) REVERT: B 459 HIS cc_start: 0.7534 (p-80) cc_final: 0.6794 (p-80) REVERT: B 543 MET cc_start: 0.6971 (pmm) cc_final: 0.6660 (ptp) REVERT: B 560 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8450 (tp40) REVERT: B 568 LEU cc_start: 0.7638 (tt) cc_final: 0.7250 (mp) REVERT: B 938 MET cc_start: 0.8722 (tpp) cc_final: 0.8230 (tpp) outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.1564 time to fit residues: 32.0833 Evaluate side-chains 118 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9642 Z= 0.158 Angle : 0.477 6.107 13172 Z= 0.256 Chirality : 0.040 0.200 1550 Planarity : 0.003 0.031 1612 Dihedral : 12.635 133.058 1470 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.68 % Allowed : 12.75 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1234 helix: 2.35 (0.19), residues: 740 sheet: -0.28 (0.45), residues: 152 loop : -0.81 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 806 HIS 0.005 0.001 HIS A 828 PHE 0.015 0.001 PHE A 864 TYR 0.011 0.001 TYR B 713 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7211 (tp-100) REVERT: A 543 MET cc_start: 0.7052 (pmm) cc_final: 0.6714 (ptp) REVERT: A 560 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8423 (tp40) REVERT: A 876 MET cc_start: 0.8939 (tpp) cc_final: 0.8529 (tpp) REVERT: A 1066 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8124 (t70) REVERT: B 437 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7284 (tp-100) REVERT: B 543 MET cc_start: 0.6868 (pmm) cc_final: 0.6625 (ptp) REVERT: B 560 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8437 (tp40) REVERT: B 876 MET cc_start: 0.8941 (tpp) cc_final: 0.8523 (tpp) REVERT: B 1052 PHE cc_start: 0.8655 (t80) cc_final: 0.8303 (t80) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.1457 time to fit residues: 28.2366 Evaluate side-chains 122 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9642 Z= 0.254 Angle : 0.527 6.437 13172 Z= 0.282 Chirality : 0.041 0.201 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.775 137.592 1470 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 14.32 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1234 helix: 2.21 (0.19), residues: 754 sheet: -0.27 (0.45), residues: 152 loop : -0.75 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.022 0.001 PHE A1052 TYR 0.019 0.002 TYR B 455 ARG 0.005 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7128 (tp-100) REVERT: A 543 MET cc_start: 0.6990 (pmm) cc_final: 0.6707 (ptp) REVERT: A 560 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8502 (tp40) REVERT: A 606 MET cc_start: 0.6154 (mpp) cc_final: 0.5817 (mtt) REVERT: A 938 MET cc_start: 0.8661 (tpp) cc_final: 0.7779 (tpp) REVERT: A 1066 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8239 (t70) REVERT: B 416 MET cc_start: 0.5128 (tmm) cc_final: 0.4787 (tpp) REVERT: B 437 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7151 (tp-100) REVERT: B 543 MET cc_start: 0.6829 (pmm) cc_final: 0.6619 (ptp) REVERT: B 560 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8482 (tp40) REVERT: B 568 LEU cc_start: 0.7677 (tt) cc_final: 0.7243 (mp) REVERT: B 886 MET cc_start: 0.8335 (ttp) cc_final: 0.8045 (tmm) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1607 time to fit residues: 28.5560 Evaluate side-chains 122 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9642 Z= 0.211 Angle : 0.508 6.642 13172 Z= 0.269 Chirality : 0.040 0.204 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.613 139.675 1470 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.68 % Allowed : 15.10 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1234 helix: 2.29 (0.19), residues: 756 sheet: -0.22 (0.45), residues: 152 loop : -0.84 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.017 0.001 PHE A1052 TYR 0.014 0.001 TYR A 455 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.066 Fit side-chains REVERT: A 416 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.4920 (tmm) REVERT: A 437 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7139 (tp-100) REVERT: A 476 MET cc_start: 0.8353 (mpp) cc_final: 0.7268 (mpp) REVERT: A 543 MET cc_start: 0.6883 (pmm) cc_final: 0.6595 (ptp) REVERT: A 560 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8504 (tp40) REVERT: A 876 MET cc_start: 0.9022 (tpp) cc_final: 0.8741 (tpp) REVERT: A 886 MET cc_start: 0.7892 (tmm) cc_final: 0.7352 (tmm) REVERT: A 925 TYR cc_start: 0.8161 (m-10) cc_final: 0.7945 (m-80) REVERT: A 1066 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8215 (t70) REVERT: B 416 MET cc_start: 0.5155 (tmm) cc_final: 0.4879 (tpp) REVERT: B 437 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7150 (tp-100) REVERT: B 476 MET cc_start: 0.8344 (mpp) cc_final: 0.7348 (mpp) REVERT: B 560 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8521 (tp40) REVERT: B 876 MET cc_start: 0.9020 (tpp) cc_final: 0.8740 (tpp) REVERT: B 886 MET cc_start: 0.8302 (ttp) cc_final: 0.8034 (tmm) REVERT: B 938 MET cc_start: 0.8563 (tpp) cc_final: 0.7598 (tpp) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.1564 time to fit residues: 29.7521 Evaluate side-chains 124 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.0770 chunk 13 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9642 Z= 0.147 Angle : 0.478 6.043 13172 Z= 0.257 Chirality : 0.040 0.210 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.034 140.016 1470 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.90 % Allowed : 16.78 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1234 helix: 2.49 (0.19), residues: 744 sheet: -0.16 (0.44), residues: 152 loop : -0.85 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.015 0.001 PHE B 772 TYR 0.015 0.001 TYR A 455 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5034 (tmm) REVERT: A 437 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7151 (tp-100) REVERT: A 543 MET cc_start: 0.6979 (pmm) cc_final: 0.6765 (ptp) REVERT: A 560 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8497 (tp40) REVERT: A 606 MET cc_start: 0.6001 (mtm) cc_final: 0.5308 (mtt) REVERT: A 876 MET cc_start: 0.8952 (tpp) cc_final: 0.8519 (tpp) REVERT: A 886 MET cc_start: 0.7839 (tmm) cc_final: 0.7317 (tmm) REVERT: A 1052 PHE cc_start: 0.8579 (t80) cc_final: 0.8220 (t80) REVERT: B 437 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7181 (tp-100) REVERT: B 560 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8510 (tp40) REVERT: B 606 MET cc_start: 0.5923 (mtm) cc_final: 0.5235 (mtt) REVERT: B 876 MET cc_start: 0.8950 (tpp) cc_final: 0.8523 (tpp) REVERT: B 886 MET cc_start: 0.8264 (ttp) cc_final: 0.8037 (tmm) REVERT: B 925 TYR cc_start: 0.8070 (m-10) cc_final: 0.7765 (m-80) REVERT: B 938 MET cc_start: 0.8565 (tpp) cc_final: 0.7667 (tpp) REVERT: B 1052 PHE cc_start: 0.8576 (t80) cc_final: 0.8208 (t80) outliers start: 17 outliers final: 15 residues processed: 125 average time/residue: 0.1625 time to fit residues: 31.4716 Evaluate side-chains 128 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 756 GLN B 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9642 Z= 0.236 Angle : 0.535 8.295 13172 Z= 0.281 Chirality : 0.040 0.181 1550 Planarity : 0.003 0.031 1612 Dihedral : 11.446 140.871 1470 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.35 % Allowed : 17.34 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1234 helix: 2.38 (0.19), residues: 746 sheet: -0.41 (0.43), residues: 152 loop : -0.72 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS A 937 PHE 0.023 0.001 PHE B1052 TYR 0.012 0.001 TYR A 613 ARG 0.004 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5095 (tmm) REVERT: A 437 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7159 (tp-100) REVERT: A 543 MET cc_start: 0.6991 (pmm) cc_final: 0.6763 (ptp) REVERT: A 560 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8504 (tp40) REVERT: A 606 MET cc_start: 0.6066 (mtm) cc_final: 0.5374 (mtt) REVERT: A 886 MET cc_start: 0.7935 (tmm) cc_final: 0.7440 (tmm) REVERT: B 437 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7213 (tp-100) REVERT: B 560 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8517 (tp40) REVERT: B 568 LEU cc_start: 0.7544 (tt) cc_final: 0.7227 (mp) REVERT: B 606 MET cc_start: 0.6103 (mtm) cc_final: 0.5363 (mtt) REVERT: B 810 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 886 MET cc_start: 0.8285 (ttp) cc_final: 0.8014 (tmm) REVERT: B 925 TYR cc_start: 0.8140 (m-10) cc_final: 0.7825 (m-80) REVERT: B 938 MET cc_start: 0.8663 (tpp) cc_final: 0.7746 (tpp) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.1656 time to fit residues: 30.0377 Evaluate side-chains 127 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9642 Z= 0.163 Angle : 0.504 8.256 13172 Z= 0.257 Chirality : 0.039 0.184 1550 Planarity : 0.003 0.031 1612 Dihedral : 11.025 141.746 1470 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.46 % Allowed : 17.56 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1234 helix: 2.46 (0.19), residues: 746 sheet: -0.37 (0.43), residues: 152 loop : -0.71 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 PHE 0.017 0.001 PHE B 772 TYR 0.013 0.001 TYR B 455 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.5115 (tmm) REVERT: A 437 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7136 (tp-100) REVERT: A 543 MET cc_start: 0.6990 (pmm) cc_final: 0.6749 (ptp) REVERT: A 560 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8498 (tp40) REVERT: A 606 MET cc_start: 0.5860 (mtm) cc_final: 0.5164 (mtt) REVERT: A 886 MET cc_start: 0.7888 (tmm) cc_final: 0.7354 (tmm) REVERT: A 1052 PHE cc_start: 0.8669 (t80) cc_final: 0.8216 (t80) REVERT: B 437 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7195 (tp-100) REVERT: B 560 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8510 (tp40) REVERT: B 606 MET cc_start: 0.5927 (mtm) cc_final: 0.5205 (mtt) REVERT: B 810 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8761 (m) REVERT: B 886 MET cc_start: 0.8259 (ttp) cc_final: 0.7992 (tmm) REVERT: B 925 TYR cc_start: 0.8107 (m-10) cc_final: 0.7809 (m-80) REVERT: B 938 MET cc_start: 0.8650 (tpp) cc_final: 0.7726 (tpp) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.1596 time to fit residues: 29.2227 Evaluate side-chains 132 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9642 Z= 0.183 Angle : 0.513 8.278 13172 Z= 0.263 Chirality : 0.039 0.184 1550 Planarity : 0.003 0.031 1612 Dihedral : 10.924 141.368 1470 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.13 % Allowed : 17.90 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1234 helix: 2.49 (0.19), residues: 744 sheet: -0.37 (0.43), residues: 152 loop : -0.66 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 PHE 0.017 0.001 PHE B 772 TYR 0.012 0.001 TYR B 455 ARG 0.003 0.000 ARG A 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.5019 (tmm) REVERT: A 437 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7174 (tp-100) REVERT: A 543 MET cc_start: 0.7008 (pmm) cc_final: 0.6806 (ptp) REVERT: A 606 MET cc_start: 0.5974 (mtm) cc_final: 0.5273 (mtt) REVERT: A 886 MET cc_start: 0.7918 (tmm) cc_final: 0.7427 (tmm) REVERT: B 437 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7216 (tp-100) REVERT: B 560 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8507 (tp40) REVERT: B 606 MET cc_start: 0.5805 (mtm) cc_final: 0.5099 (mtt) REVERT: B 810 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8761 (m) REVERT: B 886 MET cc_start: 0.8277 (ttp) cc_final: 0.8015 (tmm) REVERT: B 925 TYR cc_start: 0.8140 (m-10) cc_final: 0.7863 (m-80) REVERT: B 938 MET cc_start: 0.8705 (tpp) cc_final: 0.7738 (tpp) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.1579 time to fit residues: 28.9381 Evaluate side-chains 126 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.123499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090282 restraints weight = 20869.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093357 restraints weight = 9674.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095274 restraints weight = 6151.704| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9642 Z= 0.349 Angle : 0.603 7.790 13172 Z= 0.315 Chirality : 0.042 0.183 1550 Planarity : 0.003 0.037 1612 Dihedral : 11.203 142.521 1470 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.01 % Allowed : 18.79 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1234 helix: 2.27 (0.19), residues: 746 sheet: -0.55 (0.43), residues: 152 loop : -0.78 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 806 HIS 0.005 0.001 HIS A 937 PHE 0.026 0.002 PHE A1052 TYR 0.011 0.002 TYR B 455 ARG 0.006 0.001 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.69 seconds wall clock time: 30 minutes 50.22 seconds (1850.22 seconds total)