Starting phenix.real_space_refine on Fri Jun 5 05:13:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkq_74381/06_2026/9zkq_74381.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 113 5.16 5 C 11626 2.51 5 N 2750 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17595 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2956 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2948 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2962 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2944 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "F" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1431 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1348 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1353 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'OLC': 2, 'PLM': 4, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'OLC': 2, 'PLM': 4, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.25 Number of scatterers: 17595 At special positions: 0 Unit cell: (113.85, 120.45, 132.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 6 15.00 O 3100 8.00 N 2750 7.00 C 11626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.02 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 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: 1.66 Conformation dependent library (CDL) restraints added in 729.4 milliseconds 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 25 sheets defined 58.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.933A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.683A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 655 through 658 removed outlier: 3.685A pdb=" N SER A 658 " --> pdb=" O PHE A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 658' Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.559A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 740 through 749 removed outlier: 4.141A pdb=" N LEU A 744 " --> pdb=" O GLY A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.514A pdb=" N SER A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.749A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (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 436 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.759A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.602A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.881A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.564A pdb=" N ASN B 747 " --> pdb=" O ARG B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 4.279A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.704A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.025A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 432 Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.501A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 464 " --> pdb=" O VAL C 460 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 592 through 626 Processing helix chain 'C' and resid 632 through 637 removed outlier: 4.196A pdb=" N LYS C 637 " --> pdb=" O GLU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 657 removed outlier: 4.190A pdb=" N LYS C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.593A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 709 through 711 No H-bonds generated for 'chain 'C' and resid 709 through 711' Processing helix chain 'C' and resid 738 through 750 Processing helix chain 'C' and resid 753 through 764 removed outlier: 4.194A pdb=" N LYS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.992A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.246A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 482 through 486 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.565A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.549A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.827A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.509A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 705 through 713 removed outlier: 3.502A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 757 removed outlier: 3.561A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 4.223A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 779 removed outlier: 3.547A pdb=" N GLY D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.801A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 38 Processing helix chain 'E' and resid 56 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 88 through 107 Proline residue: E 96 - end of helix removed outlier: 3.810A pdb=" N HIS E 107 " --> pdb=" O TRP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 Processing helix chain 'F' and resid 5 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.580A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 Processing helix chain 'F' and resid 177 through 210 removed outlier: 3.642A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 41 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 148 removed outlier: 3.862A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 184 removed outlier: 3.650A pdb=" N ALA G 184 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 234 removed outlier: 3.867A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 41 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 Processing helix chain 'H' and resid 155 through 184 removed outlier: 4.032A pdb=" N LEU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 removed outlier: 4.103A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.804A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.941A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 678 through 679 removed outlier: 8.514A pdb=" N VAL A 679 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 645 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 398 removed outlier: 5.500A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 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 453 through 454 removed outlier: 3.754A pdb=" N ASP B 454 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.875A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.875A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 7.008A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 391 through 395 Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 removed outlier: 3.504A pdb=" N MET C 403 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 471 through 473 removed outlier: 4.357A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 701 removed outlier: 3.928A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C 500 " --> pdb=" O MET C 717 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 717 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.559A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 475 through 480 removed outlier: 8.003A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 480 removed outlier: 8.003A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 502 through 505 removed outlier: 3.816A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.598A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.950A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 101 through 102 removed outlier: 3.541A pdb=" N CYS G 90 " --> pdb=" O HIS G 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 82 through 83 1034 hydrogen bonds defined for protein. 3015 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: 2.98 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2964 1.33 - 1.45: 4842 1.45 - 1.58: 9961 1.58 - 1.70: 12 1.70 - 1.83: 173 Bond restraints: 17952 Sorted by residual: bond pdb=" O12 POV C 905 " pdb=" P POV C 905 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" O12 POV A1004 " pdb=" P POV A1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" O12 POV C 904 " pdb=" P POV C 904 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" O12 POV H 501 " pdb=" P POV H 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" O12 POV A1003 " pdb=" P POV A1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.43e+00 ... (remaining 17947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 23648 2.33 - 4.65: 490 4.65 - 6.98: 73 6.98 - 9.31: 25 9.31 - 11.63: 2 Bond angle restraints: 24238 Sorted by residual: angle pdb=" C GLU D 755 " pdb=" N GLN D 756 " pdb=" CA GLN D 756 " ideal model delta sigma weight residual 121.54 112.66 8.88 1.91e+00 2.74e-01 2.16e+01 angle pdb=" N VAL C 677 " pdb=" CA VAL C 677 " pdb=" C VAL C 677 " ideal model delta sigma weight residual 113.71 109.42 4.29 9.50e-01 1.11e+00 2.04e+01 angle pdb=" C ARG C 541 " pdb=" N PHE C 542 " pdb=" CA PHE C 542 " ideal model delta sigma weight residual 121.58 113.35 8.23 1.95e+00 2.63e-01 1.78e+01 angle pdb=" CB LYS B 509 " pdb=" CG LYS B 509 " pdb=" CD LYS B 509 " ideal model delta sigma weight residual 111.30 120.97 -9.67 2.30e+00 1.89e-01 1.77e+01 angle pdb=" N GLU F 191 " pdb=" CA GLU F 191 " pdb=" CB GLU F 191 " ideal model delta sigma weight residual 110.28 116.41 -6.13 1.55e+00 4.16e-01 1.56e+01 ... (remaining 24233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 10297 35.20 - 70.40: 169 70.40 - 105.60: 11 105.60 - 140.81: 20 140.81 - 176.01: 5 Dihedral angle restraints: 10502 sinusoidal: 3951 harmonic: 6551 Sorted by residual: dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -175.47 89.47 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 156.85 -63.85 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS G 52 " pdb=" SG CYS G 52 " pdb=" SG CYS G 91 " pdb=" CB CYS G 91 " ideal model delta sinusoidal sigma weight residual -86.00 -143.51 57.51 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 10499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2419 0.069 - 0.139: 317 0.139 - 0.208: 21 0.208 - 0.278: 6 0.278 - 0.347: 2 Chirality restraints: 2765 Sorted by residual: chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB ILE B 489 " pdb=" CA ILE B 489 " pdb=" CG1 ILE B 489 " pdb=" CG2 ILE B 489 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE G 173 " pdb=" CA ILE G 173 " pdb=" CG1 ILE G 173 " pdb=" CG2 ILE G 173 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2762 not shown) Planarity restraints: 2945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 679 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 106 " -0.057 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO G 107 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO G 107 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 107 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO D 717 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.044 5.00e-02 4.00e+02 ... (remaining 2942 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2266 2.75 - 3.29: 17617 3.29 - 3.83: 29153 3.83 - 4.36: 33125 4.36 - 4.90: 57374 Nonbonded interactions: 139535 Sorted by model distance: nonbonded pdb=" OE2 GLU C 706 " pdb=" OH TYR C 764 " model vdw 2.218 3.040 nonbonded pdb=" O GLN G 20 " pdb=" OG1 THR G 24 " model vdw 2.267 3.040 nonbonded pdb=" OG SER B 592 " pdb=" OD2 ASP C 586 " model vdw 2.271 3.040 nonbonded pdb=" O PRO A 516 " pdb=" ND2 ASN A 615 " model vdw 2.279 3.120 nonbonded pdb=" NE2 GLN C 638 " pdb=" O ILE C 641 " model vdw 2.292 3.120 ... (remaining 139530 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 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 444 or (resid 445 and (name N or name CA or name C or name O or name \ CB )) or resid 446 through 450 or resid 452 through 454 or resid 456 through 46 \ 1 or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 481 or (resid 482 through \ 483 and (name N or name CA or name C or name O or name CB )) or resid 484 throu \ gh 543 or (resid 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N or nam \ e CA or name C or name O or name CB )) or resid 631 through 635 or (resid 637 th \ rough 640 and (name N or name CA or name C or name O or name CB )) or resid 641 \ through 646 or resid 649 or (resid 650 and (name N or name CA or name C or name \ O or name CB )) or resid 651 or (resid 652 through 653 and (name N or name CA or \ name C or name O or name CB )) or resid 654 through 663 or resid 665 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 675 or (resid 676 and (name N or name CA or name C or name O or na \ me CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 through \ 689 or (resid 690 through 693 and (name N or name CA or name C or name O or name \ CB )) or resid 694 through 733 or (resid 734 and (name N or name CA or name C o \ r name O or name CB )) or resid 735 through 736 or resid 738 through 739 or resi \ d 742 through 749 or resid 751 through 753 or resid 755 through 759 or resid 761 \ through 771 or resid 776 through 777 or resid 779 through 795 or resid 797 thro \ ugh 811 or (resid 812 through 813 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'B' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 48 or (resid 449 and (name N or name CA or name C or name O or name CB )) or res \ id 450 through 454 or (resid 456 through 458 and (name N or name CA or name C or \ name O or name CB )) or resid 460 through 470 or resid 472 through 473 or resid \ 475 or resid 477 through 486 or (resid 487 and (name N or name CA or name C or \ name O or name CB )) or resid 488 through 507 or (resid 508 through 509 and (nam \ e N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 585 or \ resid 587 through 639 or resid 641 through 650 or resid 653 through 659 or (res \ id 660 through 661 and (name N or name CA or name C or name O or name CB )) or r \ esid 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) \ or resid 664 through 667 or resid 669 through 674 or resid 676 through 684 or (r \ esid 685 and (name N or name CA or name C or name O or name CB )) or resid 686 o \ r (resid 688 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 89 or (resid 692 and (name N or name CA or name C or name O or name CB )) or res \ id 693 through 695 or (resid 696 through 697 and (name N or name CA or name C or \ name O or name CB )) or resid 698 through 714 or (resid 715 through 716 and (na \ me N or name CA or name C or name O or name CB )) or resid 717 through 740 or re \ sid 742 or (resid 743 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 753 or resid 755 through 757 or resid 759 through 763 or res \ id 765 through 768 or (resid 769 and (name N or name CA or name C or name O or n \ ame CB )) or resid 770 through 775 or resid 780 through 781 or (resid 783 throug \ h 784 and (name N or name CA or name C or name O or name CB )) or resid 785 thro \ ugh 799 or resid 801 through 817)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 444 or (resid 445 and (name N or name CA or name C or name O or name \ CB )) or resid 446 through 450 or resid 452 through 454 or resid 456 through 46 \ 1 or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 481 or (resid 482 through \ 483 and (name N or name CA or name C or name O or name CB )) or resid 484 throu \ gh 543 or (resid 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N or nam \ e CA or name C or name O or name CB )) or resid 631 through 635 or (resid 637 th \ rough 640 and (name N or name CA or name C or name O or name CB )) or resid 641 \ through 646 or resid 649 or (resid 650 and (name N or name CA or name C or name \ O or name CB )) or resid 651 or (resid 652 through 653 and (name N or name CA or \ name C or name O or name CB )) or resid 654 through 663 or resid 665 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 675 or (resid 676 and (name N or name CA or name C or name O or na \ me CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 through \ 689 or (resid 690 through 693 and (name N or name CA or name C or name O or name \ CB )) or resid 694 through 733 or (resid 734 and (name N or name CA or name C o \ r name O or name CB )) or resid 735 through 736 or resid 738 or (resid 739 and ( \ name N or name CA or name C or name O or name CB )) or resid 742 through 749 or \ resid 751 through 753 or resid 755 through 759 or resid 761 through 771 or resid \ 776 through 777 or resid 779 through 795 or resid 797 through 811 or (resid 812 \ through 813 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 47 \ 7 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 507 or (resid 508 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 or (resid 511 and (name N or name \ CA or name C or name O or name CB )) or resid 512 through 585 or resid 587 throu \ gh 639 or resid 641 through 650 or resid 653 through 659 or (resid 660 through 6 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 667 or resid 669 through 674 or resid 676 through 684 or (resid 685 and (na \ me N or name CA or name C or name O or name CB )) or resid 686 or (resid 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 692 \ and (name N or name CA or name C or name O or name CB )) or resid 693 through 6 \ 95 or (resid 696 through 697 and (name N or name CA or name C or name O or name \ CB )) or resid 698 through 714 or (resid 715 through 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 740 or resid 742 or (resi \ d 743 and (name N or name CA or name C or name O or name CB )) or resid 746 thro \ ugh 753 or resid 755 through 757 or resid 759 through 763 or resid 765 through 7 \ 68 or (resid 769 and (name N or name CA or name C or name O or name CB )) or res \ id 770 through 775 or resid 780 through 781 or (resid 783 through 784 and (name \ N or name CA or name C or name O or name CB )) or resid 785 through 799 or resid \ 801 through 817)) } ncs_group { reference = (chain 'G' and (resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 501)) selection = (chain 'H' and (resid 15 through 185 or resid 197 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.005 0.074 17962 Z= 0.234 Angle : 0.825 11.633 24258 Z= 0.422 Chirality : 0.048 0.347 2765 Planarity : 0.007 0.093 2945 Dihedral : 15.683 176.008 6296 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2242 helix: 0.52 (0.14), residues: 1276 sheet: -2.29 (0.43), residues: 133 loop : -2.01 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 590 TYR 0.045 0.002 TYR H 226 PHE 0.028 0.002 PHE D 438 TRP 0.029 0.002 TRP D 766 HIS 0.019 0.003 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (17952) covalent geometry : angle 0.82402 / 0.42 (24238) SS BOND : bond 0.00479 / 0.29 ( 10) SS BOND : angle 1.69339 / 1.04 ( 20) hydrogen bonds : bond 0.14326 / 9.66 ( 1032) hydrogen bonds : angle 6.16127 / 4.33 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.665 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: A 492 MET cc_start: 0.8600 (mtt) cc_final: 0.8383 (mtp) REVERT: A 567 PHE cc_start: 0.7729 (m-80) cc_final: 0.7397 (m-80) REVERT: A 666 MET cc_start: 0.7432 (mtm) cc_final: 0.7011 (ttm) REVERT: A 784 SER cc_start: 0.8410 (p) cc_final: 0.8131 (m) REVERT: B 407 MET cc_start: 0.7797 (mtp) cc_final: 0.7286 (mtt) REVERT: B 489 ILE cc_start: 0.8231 (tp) cc_final: 0.8014 (tp) REVERT: B 630 VAL cc_start: 0.7227 (m) cc_final: 0.6743 (p) REVERT: B 756 GLN cc_start: 0.8560 (mt0) cc_final: 0.8106 (mt0) REVERT: C 496 ILE cc_start: 0.8522 (mm) cc_final: 0.8220 (mm) REVERT: C 523 MET cc_start: 0.7218 (tpt) cc_final: 0.6555 (ttm) REVERT: C 590 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7982 (ttm-80) REVERT: C 646 LEU cc_start: 0.8278 (mm) cc_final: 0.7623 (tp) REVERT: C 696 TYR cc_start: 0.8504 (t80) cc_final: 0.8252 (t80) REVERT: D 400 ILE cc_start: 0.7433 (tp) cc_final: 0.7227 (mm) REVERT: D 427 ASP cc_start: 0.8219 (m-30) cc_final: 0.7661 (p0) REVERT: D 484 VAL cc_start: 0.9110 (m) cc_final: 0.8895 (p) REVERT: D 688 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8363 (tt0) REVERT: D 761 LYS cc_start: 0.8336 (mptt) cc_final: 0.8109 (mmtt) REVERT: D 762 LEU cc_start: 0.8715 (tp) cc_final: 0.7612 (tp) REVERT: D 766 TRP cc_start: 0.7299 (m100) cc_final: 0.6797 (m-90) REVERT: D 767 TRP cc_start: 0.6397 (m100) cc_final: 0.5495 (m100) REVERT: E 63 LEU cc_start: 0.8805 (mm) cc_final: 0.8568 (tt) REVERT: E 84 CYS cc_start: 0.7637 (m) cc_final: 0.7396 (m) REVERT: E 99 PHE cc_start: 0.9011 (m-80) cc_final: 0.8705 (m-80) REVERT: E 123 MET cc_start: 0.4350 (mmt) cc_final: 0.4106 (pmm) REVERT: F 6 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8159 (mmm-85) REVERT: F 78 LYS cc_start: 0.6987 (ptpt) cc_final: 0.6718 (ptpt) REVERT: F 96 TYR cc_start: 0.8418 (t80) cc_final: 0.8068 (t80) REVERT: F 99 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8383 (mtp-110) REVERT: F 117 MET cc_start: 0.7656 (mpp) cc_final: 0.7422 (mtm) REVERT: F 128 TYR cc_start: 0.8508 (m-80) cc_final: 0.8153 (m-80) REVERT: F 160 ASN cc_start: 0.8637 (m110) cc_final: 0.8353 (m-40) REVERT: F 174 TYR cc_start: 0.6208 (m-80) cc_final: 0.5839 (t80) REVERT: F 178 TRP cc_start: 0.8004 (p-90) cc_final: 0.7758 (p-90) REVERT: H 29 PHE cc_start: 0.7433 (t80) cc_final: 0.7114 (t80) REVERT: H 106 PHE cc_start: 0.7741 (m-10) cc_final: 0.7523 (m-80) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1398 time to fit residues: 93.1935 Evaluate side-chains 343 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 ASN G 156 ASN G 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123402 restraints weight = 29772.701| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.15 r_work: 0.3378 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17962 Z= 0.130 Angle : 0.579 8.523 24258 Z= 0.300 Chirality : 0.041 0.213 2765 Planarity : 0.005 0.067 2945 Dihedral : 13.475 167.690 2914 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 10.11 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2242 helix: 1.27 (0.15), residues: 1316 sheet: -2.33 (0.43), residues: 123 loop : -1.88 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 65 TYR 0.035 0.002 TYR H 226 PHE 0.022 0.001 PHE C 542 TRP 0.018 0.001 TRP D 766 HIS 0.006 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17952) covalent geometry : angle 0.57737 / 0.30 (24238) SS BOND : bond 0.00443 / 0.28 ( 10) SS BOND : angle 1.77339 / 1.13 ( 20) hydrogen bonds : bond 0.04177 / 2.79 ( 1032) hydrogen bonds : angle 4.39624 / 3.08 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 0.631 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: A 666 MET cc_start: 0.8399 (mtm) cc_final: 0.7931 (ttm) REVERT: A 784 SER cc_start: 0.8766 (p) cc_final: 0.8315 (m) REVERT: C 523 MET cc_start: 0.7815 (tpt) cc_final: 0.7389 (ttm) REVERT: D 484 VAL cc_start: 0.8842 (m) cc_final: 0.8641 (p) REVERT: D 585 MET cc_start: 0.9143 (mmt) cc_final: 0.8780 (mmt) REVERT: D 762 LEU cc_start: 0.8739 (tp) cc_final: 0.8454 (tp) REVERT: D 766 TRP cc_start: 0.7839 (m100) cc_final: 0.7429 (m-10) REVERT: D 767 TRP cc_start: 0.7036 (m100) cc_final: 0.6278 (m100) REVERT: E 63 LEU cc_start: 0.8707 (mm) cc_final: 0.8506 (tt) REVERT: E 99 PHE cc_start: 0.8892 (m-80) cc_final: 0.8470 (m-80) REVERT: F 9 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: F 96 TYR cc_start: 0.8136 (t80) cc_final: 0.7922 (t80) REVERT: F 117 MET cc_start: 0.7719 (mpp) cc_final: 0.7436 (mtm) REVERT: F 128 TYR cc_start: 0.8375 (m-80) cc_final: 0.8041 (m-80) REVERT: F 156 TYR cc_start: 0.8653 (t80) cc_final: 0.8411 (t80) REVERT: F 160 ASN cc_start: 0.8968 (m110) cc_final: 0.8712 (m-40) REVERT: F 176 TYR cc_start: 0.7229 (m-80) cc_final: 0.6778 (m-80) REVERT: H 29 PHE cc_start: 0.7210 (t80) cc_final: 0.6892 (t80) REVERT: H 106 PHE cc_start: 0.7993 (m-10) cc_final: 0.7784 (m-80) REVERT: H 201 TYR cc_start: 0.8055 (m-80) cc_final: 0.7850 (m-80) REVERT: H 226 TYR cc_start: 0.8495 (t80) cc_final: 0.8262 (t80) outliers start: 29 outliers final: 19 residues processed: 394 average time/residue: 0.1376 time to fit residues: 81.6306 Evaluate side-chains 359 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 170 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN A 752 GLN B 756 GLN C 457 ASN D 756 GLN E 107 HIS G 172 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.163851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120890 restraints weight = 29937.532| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.78 r_work: 0.3416 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17962 Z= 0.207 Angle : 0.611 9.129 24258 Z= 0.318 Chirality : 0.042 0.177 2765 Planarity : 0.005 0.063 2945 Dihedral : 12.753 149.760 2914 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.27 % Allowed : 12.60 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2242 helix: 1.34 (0.15), residues: 1306 sheet: -2.36 (0.44), residues: 119 loop : -1.82 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 743 TYR 0.029 0.002 TYR H 226 PHE 0.022 0.002 PHE C 542 TRP 0.022 0.001 TRP D 766 HIS 0.006 0.002 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (17952) covalent geometry : angle 0.60900 / 0.32 (24238) SS BOND : bond 0.01080 / 0.66 ( 10) SS BOND : angle 1.66585 / 1.02 ( 20) hydrogen bonds : bond 0.04323 / 2.89 ( 1032) hydrogen bonds : angle 4.27418 / 2.99 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 440 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (p90) REVERT: D 503 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.6868 (tpp) REVERT: D 767 TRP cc_start: 0.7193 (m100) cc_final: 0.6466 (m100) REVERT: E 99 PHE cc_start: 0.8811 (m-80) cc_final: 0.8472 (m-80) REVERT: E 136 TRP cc_start: 0.7625 (m100) cc_final: 0.7064 (m-10) REVERT: F 117 MET cc_start: 0.7714 (mpp) cc_final: 0.7428 (mtm) REVERT: F 126 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: F 128 TYR cc_start: 0.8221 (m-80) cc_final: 0.7928 (m-80) REVERT: F 191 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: H 29 PHE cc_start: 0.7123 (t80) cc_final: 0.6869 (t80) outliers start: 55 outliers final: 36 residues processed: 380 average time/residue: 0.1383 time to fit residues: 78.7579 Evaluate side-chains 366 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 457 ASN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 45 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 GLN ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121728 restraints weight = 29995.079| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.78 r_work: 0.3432 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17962 Z= 0.155 Angle : 0.577 10.861 24258 Z= 0.300 Chirality : 0.041 0.222 2765 Planarity : 0.004 0.062 2945 Dihedral : 12.393 140.784 2914 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 2.50 % Allowed : 15.58 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2242 helix: 1.39 (0.15), residues: 1314 sheet: -2.49 (0.47), residues: 101 loop : -1.80 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 590 TYR 0.026 0.002 TYR H 226 PHE 0.022 0.001 PHE G 212 TRP 0.023 0.001 TRP A 762 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (17952) covalent geometry : angle 0.57558 / 0.30 (24238) SS BOND : bond 0.00701 / 0.42 ( 10) SS BOND : angle 1.63133 / 1.03 ( 20) hydrogen bonds : bond 0.04017 / 2.71 ( 1032) hydrogen bonds : angle 4.20140 / 2.93 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 347 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.8611 (mtm) cc_final: 0.8258 (ttm) REVERT: B 440 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7807 (p90) REVERT: B 590 ASP cc_start: 0.6553 (t0) cc_final: 0.6327 (t0) REVERT: C 403 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7401 (mtp) REVERT: C 523 MET cc_start: 0.7861 (tpt) cc_final: 0.7480 (ttm) REVERT: D 728 ASP cc_start: 0.7697 (t0) cc_final: 0.7475 (t0) REVERT: D 752 LYS cc_start: 0.9186 (tppt) cc_final: 0.8985 (tppt) REVERT: D 767 TRP cc_start: 0.7141 (m100) cc_final: 0.6557 (m100) REVERT: E 99 PHE cc_start: 0.8791 (m-80) cc_final: 0.8468 (m-80) REVERT: E 136 TRP cc_start: 0.7637 (m100) cc_final: 0.7068 (m-10) REVERT: F 117 MET cc_start: 0.7706 (mpp) cc_final: 0.7381 (mtm) REVERT: F 120 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8131 (tt) REVERT: F 126 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: F 128 TYR cc_start: 0.8194 (m-80) cc_final: 0.7888 (m-80) REVERT: F 191 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: G 118 GLU cc_start: 0.6989 (pp20) cc_final: 0.6670 (pp20) REVERT: H 29 PHE cc_start: 0.7121 (t80) cc_final: 0.6872 (t80) outliers start: 42 outliers final: 30 residues processed: 372 average time/residue: 0.1394 time to fit residues: 78.0029 Evaluate side-chains 363 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 192 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120019 restraints weight = 29834.715| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.76 r_work: 0.3405 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17962 Z= 0.188 Angle : 0.605 10.789 24258 Z= 0.314 Chirality : 0.042 0.206 2765 Planarity : 0.004 0.060 2945 Dihedral : 12.340 130.479 2914 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 3.21 % Allowed : 17.12 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2242 helix: 1.42 (0.15), residues: 1303 sheet: -2.43 (0.44), residues: 119 loop : -1.84 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 149 TYR 0.028 0.002 TYR H 226 PHE 0.023 0.002 PHE G 212 TRP 0.027 0.001 TRP D 766 HIS 0.004 0.002 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (17952) covalent geometry : angle 0.60120 / 0.31 (24238) SS BOND : bond 0.01053 / 0.64 ( 10) SS BOND : angle 2.34358 / 1.42 ( 20) hydrogen bonds : bond 0.04139 / 2.79 ( 1032) hydrogen bonds : angle 4.21171 / 2.94 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 0.526 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: B 463 MET cc_start: 0.7896 (mtt) cc_final: 0.7686 (mtt) REVERT: B 491 PHE cc_start: 0.8167 (m-10) cc_final: 0.7926 (m-10) REVERT: C 638 GLN cc_start: 0.7017 (pp30) cc_final: 0.6770 (pp30) REVERT: D 767 TRP cc_start: 0.7243 (m100) cc_final: 0.6660 (m100) REVERT: E 99 PHE cc_start: 0.8827 (m-80) cc_final: 0.8476 (m-80) REVERT: E 136 TRP cc_start: 0.7656 (m100) cc_final: 0.7124 (m-10) REVERT: F 95 GLU cc_start: 0.7373 (pp20) cc_final: 0.6756 (pp20) REVERT: F 128 TYR cc_start: 0.8188 (m-80) cc_final: 0.7883 (m-80) REVERT: F 191 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: G 231 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7468 (ttt180) REVERT: H 29 PHE cc_start: 0.7156 (t80) cc_final: 0.6931 (t80) outliers start: 54 outliers final: 38 residues processed: 376 average time/residue: 0.1367 time to fit residues: 77.2588 Evaluate side-chains 358 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 123 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 GLN ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.161458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118571 restraints weight = 29812.220| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.75 r_work: 0.3379 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17962 Z= 0.222 Angle : 0.648 11.808 24258 Z= 0.335 Chirality : 0.043 0.279 2765 Planarity : 0.004 0.056 2945 Dihedral : 12.770 128.957 2914 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 4.04 % Allowed : 17.54 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2242 helix: 1.32 (0.14), residues: 1307 sheet: -2.51 (0.47), residues: 101 loop : -1.91 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 149 TYR 0.023 0.002 TYR G 43 PHE 0.038 0.002 PHE H 165 TRP 0.035 0.001 TRP D 766 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (17952) covalent geometry : angle 0.64392 / 0.33 (24238) SS BOND : bond 0.00915 / 0.55 ( 10) SS BOND : angle 2.69519 / 1.63 ( 20) hydrogen bonds : bond 0.04320 / 2.91 ( 1032) hydrogen bonds : angle 4.29585 / 3.01 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 331 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8417 (tmt170) REVERT: A 670 MET cc_start: 0.8123 (mtm) cc_final: 0.7907 (mtp) REVERT: B 450 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.4941 (t80) REVERT: C 738 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6382 (pp) REVERT: D 756 GLN cc_start: 0.8283 (mt0) cc_final: 0.8038 (mt0) REVERT: D 767 TRP cc_start: 0.7273 (m100) cc_final: 0.6644 (m100) REVERT: E 99 PHE cc_start: 0.8839 (m-80) cc_final: 0.8491 (m-80) REVERT: E 136 TRP cc_start: 0.7676 (m100) cc_final: 0.7141 (m-10) REVERT: F 95 GLU cc_start: 0.7345 (pp20) cc_final: 0.6731 (pp20) REVERT: F 117 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: F 126 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: F 128 TYR cc_start: 0.8144 (m-80) cc_final: 0.7833 (m-80) REVERT: F 151 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7994 (mt) REVERT: F 191 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: H 159 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 68 outliers final: 50 residues processed: 377 average time/residue: 0.1328 time to fit residues: 75.7809 Evaluate side-chains 370 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 128 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 122 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 709 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119568 restraints weight = 30135.859| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.08 r_work: 0.3342 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17962 Z= 0.146 Angle : 0.619 13.687 24258 Z= 0.316 Chirality : 0.042 0.342 2765 Planarity : 0.004 0.056 2945 Dihedral : 12.222 128.323 2914 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 3.09 % Allowed : 19.74 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2242 helix: 1.48 (0.15), residues: 1309 sheet: -2.53 (0.47), residues: 101 loop : -1.85 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 149 TYR 0.023 0.001 TYR C 519 PHE 0.036 0.002 PHE H 165 TRP 0.030 0.001 TRP D 766 HIS 0.024 0.002 HIS F 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17952) covalent geometry : angle 0.61172 / 0.31 (24238) SS BOND : bond 0.01172 / 0.72 ( 10) SS BOND : angle 3.35488 / 2.04 ( 20) hydrogen bonds : bond 0.03970 / 2.70 ( 1032) hydrogen bonds : angle 4.15538 / 2.90 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 0.563 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: A 666 MET cc_start: 0.8626 (mtm) cc_final: 0.8338 (ttm) REVERT: A 670 MET cc_start: 0.8068 (mtm) cc_final: 0.7857 (mtp) REVERT: B 450 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.4929 (t80) REVERT: B 502 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 391 TYR cc_start: 0.7688 (t80) cc_final: 0.7029 (t80) REVERT: C 669 TYR cc_start: 0.8114 (t80) cc_final: 0.7899 (t80) REVERT: C 738 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6188 (pp) REVERT: D 767 TRP cc_start: 0.7178 (m100) cc_final: 0.6559 (m100) REVERT: E 99 PHE cc_start: 0.8909 (m-80) cc_final: 0.8511 (m-80) REVERT: E 136 TRP cc_start: 0.7739 (m100) cc_final: 0.7198 (m-10) REVERT: F 95 GLU cc_start: 0.7516 (pp20) cc_final: 0.6838 (pp20) REVERT: F 126 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: F 128 TYR cc_start: 0.8158 (m-80) cc_final: 0.7859 (m-80) REVERT: F 134 ILE cc_start: 0.8630 (pt) cc_final: 0.8207 (tp) REVERT: F 191 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: H 159 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7446 (tt) outliers start: 52 outliers final: 42 residues processed: 365 average time/residue: 0.1390 time to fit residues: 76.6739 Evaluate side-chains 367 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 142 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 709 ASN D 756 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.160862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119815 restraints weight = 29561.503| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.97 r_work: 0.3345 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17962 Z= 0.148 Angle : 0.629 18.419 24258 Z= 0.318 Chirality : 0.042 0.324 2765 Planarity : 0.004 0.054 2945 Dihedral : 11.790 126.414 2914 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 3.39 % Allowed : 20.04 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2242 helix: 1.53 (0.14), residues: 1312 sheet: -2.63 (0.46), residues: 101 loop : -1.82 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 204 TYR 0.023 0.001 TYR H 119 PHE 0.038 0.002 PHE G 212 TRP 0.032 0.001 TRP D 766 HIS 0.007 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (17952) covalent geometry : angle 0.62219 / 0.31 (24238) SS BOND : bond 0.00700 / 0.43 ( 10) SS BOND : angle 3.28066 / 1.98 ( 20) hydrogen bonds : bond 0.03901 / 2.65 ( 1032) hydrogen bonds : angle 4.09762 / 2.87 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 0.714 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: A 437 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8441 (tmt170) REVERT: B 450 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5145 (t80) REVERT: B 502 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 767 TRP cc_start: 0.7156 (m100) cc_final: 0.6185 (m100) REVERT: C 391 TYR cc_start: 0.7635 (t80) cc_final: 0.7190 (t80) REVERT: C 717 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7342 (pmm) REVERT: C 738 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6289 (pp) REVERT: D 767 TRP cc_start: 0.7134 (m100) cc_final: 0.6506 (m100) REVERT: E 99 PHE cc_start: 0.8924 (m-80) cc_final: 0.8507 (m-80) REVERT: E 136 TRP cc_start: 0.7790 (m100) cc_final: 0.7215 (m-10) REVERT: F 95 GLU cc_start: 0.7465 (pp20) cc_final: 0.6853 (pp20) REVERT: F 126 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: F 134 ILE cc_start: 0.8662 (pt) cc_final: 0.8252 (tp) REVERT: F 151 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8046 (mt) REVERT: F 191 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: H 159 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7426 (tt) outliers start: 57 outliers final: 45 residues processed: 366 average time/residue: 0.1388 time to fit residues: 76.7395 Evaluate side-chains 372 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 132 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 199 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119841 restraints weight = 29620.960| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.04 r_work: 0.3333 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17962 Z= 0.168 Angle : 0.630 14.190 24258 Z= 0.320 Chirality : 0.042 0.249 2765 Planarity : 0.004 0.054 2945 Dihedral : 11.704 124.576 2914 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 3.51 % Allowed : 20.15 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2242 helix: 1.50 (0.14), residues: 1312 sheet: -2.60 (0.47), residues: 101 loop : -1.84 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 149 TYR 0.022 0.002 TYR H 119 PHE 0.040 0.002 PHE G 212 TRP 0.035 0.001 TRP D 766 HIS 0.012 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (17952) covalent geometry : angle 0.62566 / 0.32 (24238) SS BOND : bond 0.00514 / 0.30 ( 10) SS BOND : angle 2.67382 / 1.62 ( 20) hydrogen bonds : bond 0.03988 / 2.71 ( 1032) hydrogen bonds : angle 4.12182 / 2.88 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 319 time to evaluate : 0.736 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: A 437 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8403 (tmt170) REVERT: B 450 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5254 (t80) REVERT: B 502 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8609 (mt) REVERT: C 391 TYR cc_start: 0.7652 (t80) cc_final: 0.7299 (t80) REVERT: C 717 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7326 (pmm) REVERT: C 738 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6306 (pp) REVERT: D 427 ASP cc_start: 0.8432 (m-30) cc_final: 0.8014 (m-30) REVERT: D 767 TRP cc_start: 0.7191 (m100) cc_final: 0.6558 (m100) REVERT: E 99 PHE cc_start: 0.8935 (m-80) cc_final: 0.8538 (m-80) REVERT: E 136 TRP cc_start: 0.7789 (m100) cc_final: 0.7219 (m-10) REVERT: F 95 GLU cc_start: 0.7525 (pp20) cc_final: 0.6882 (pp20) REVERT: F 128 TYR cc_start: 0.8286 (m-80) cc_final: 0.8022 (m-80) REVERT: F 134 ILE cc_start: 0.8641 (pt) cc_final: 0.8233 (tp) REVERT: F 151 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8072 (mt) REVERT: F 176 TYR cc_start: 0.7603 (m-80) cc_final: 0.7343 (m-80) REVERT: F 191 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: G 155 ARG cc_start: 0.5034 (mpp-170) cc_final: 0.4553 (mtm180) REVERT: H 159 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7479 (tt) outliers start: 59 outliers final: 50 residues processed: 359 average time/residue: 0.1281 time to fit residues: 69.9040 Evaluate side-chains 367 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 116 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN B 418 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.160298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119167 restraints weight = 29546.982| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.98 r_work: 0.3333 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17962 Z= 0.173 Angle : 0.647 13.485 24258 Z= 0.329 Chirality : 0.043 0.285 2765 Planarity : 0.004 0.054 2945 Dihedral : 11.625 122.492 2914 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.63 % Allowed : 20.51 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2242 helix: 1.47 (0.14), residues: 1324 sheet: -2.55 (0.48), residues: 101 loop : -1.86 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 149 TYR 0.026 0.002 TYR F 176 PHE 0.038 0.002 PHE G 212 TRP 0.037 0.001 TRP D 766 HIS 0.010 0.002 HIS F 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (17952) covalent geometry : angle 0.64327 / 0.33 (24238) SS BOND : bond 0.00536 / 0.32 ( 10) SS BOND : angle 2.39373 / 1.46 ( 20) hydrogen bonds : bond 0.04017 / 2.73 ( 1032) hydrogen bonds : angle 4.16597 / 2.90 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.666 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: B 450 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5546 (t80) REVERT: B 502 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8599 (mt) REVERT: C 391 TYR cc_start: 0.7658 (t80) cc_final: 0.7389 (t80) REVERT: C 717 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7310 (pmm) REVERT: C 738 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6320 (pp) REVERT: D 427 ASP cc_start: 0.8438 (m-30) cc_final: 0.8017 (m-30) REVERT: D 756 GLN cc_start: 0.8319 (mt0) cc_final: 0.7993 (mt0) REVERT: D 767 TRP cc_start: 0.7168 (m100) cc_final: 0.6542 (m100) REVERT: E 99 PHE cc_start: 0.8922 (m-80) cc_final: 0.8518 (m-80) REVERT: E 136 TRP cc_start: 0.7797 (m100) cc_final: 0.7220 (m-10) REVERT: F 95 GLU cc_start: 0.7536 (pp20) cc_final: 0.6889 (pp20) REVERT: F 126 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: F 134 ILE cc_start: 0.8646 (pt) cc_final: 0.8235 (tp) REVERT: F 151 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8063 (mt) REVERT: F 174 TYR cc_start: 0.7869 (t80) cc_final: 0.7216 (t80) REVERT: F 191 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: H 159 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7482 (tt) outliers start: 61 outliers final: 51 residues processed: 360 average time/residue: 0.1306 time to fit residues: 71.4405 Evaluate side-chains 373 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 122 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN D 756 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119499 restraints weight = 30186.362| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.96 r_work: 0.3333 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17962 Z= 0.157 Angle : 0.644 13.597 24258 Z= 0.328 Chirality : 0.043 0.325 2765 Planarity : 0.004 0.054 2945 Dihedral : 11.363 119.731 2914 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 3.45 % Allowed : 20.87 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2242 helix: 1.55 (0.14), residues: 1320 sheet: -2.55 (0.48), residues: 101 loop : -1.84 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 204 TYR 0.026 0.001 TYR H 119 PHE 0.031 0.002 PHE H 165 TRP 0.036 0.001 TRP D 766 HIS 0.014 0.002 HIS F 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (17952) covalent geometry : angle 0.64095 / 0.33 (24238) SS BOND : bond 0.00520 / 0.30 ( 10) SS BOND : angle 2.12838 / 1.30 ( 20) hydrogen bonds : bond 0.03966 / 2.70 ( 1032) hydrogen bonds : angle 4.13902 / 2.88 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4535.88 seconds wall clock time: 78 minutes 25.26 seconds (4705.26 seconds total)