Starting phenix.real_space_refine on Fri Jun 5 05:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkm_74377/06_2026/9zkm_74377.map" } resolution = 3.13 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= 0.023 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 8 5.49 5 S 107 5.16 5 C 11765 2.51 5 N 2787 2.21 5 O 3155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s 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: 17822 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2973 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2983 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2978 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'PHE:plan': 1, 'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "E" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1428 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1442 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1174 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1172 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 168 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 39 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: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 167 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 172 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 168 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.26 Number of scatterers: 17822 At special positions: 0 Unit cell: (112.2, 119.625, 133.65, 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 107 16.00 P 8 15.00 O 3155 8.00 N 2787 7.00 C 11765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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 E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " 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=2.04 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=2.03 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=2.05 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: 1.63 Conformation dependent library (CDL) restraints added in 815.3 milliseconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 21 sheets defined 58.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.688A pdb=" N GLY A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) 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 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.597A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.511A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.674A pdb=" N LYS A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.687A pdb=" N ILE A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 788 through 813 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.810A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.650A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.868A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.580A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.958A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 705 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 removed outlier: 4.063A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.866A 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 433 removed outlier: 3.675A pdb=" N GLU C 423 " --> pdb=" O GLY C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.710A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.609A pdb=" N GLU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 removed outlier: 3.844A pdb=" N ARG C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.717A pdb=" N GLN C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.600A pdb=" N LYS C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.582A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.527A pdb=" N GLY D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.773A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.602A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.998A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 4.296A 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 706 through 714 Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 774 through 780 removed outlier: 3.909A pdb=" N GLY D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.502A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 800 " --> pdb=" O PHE D 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 29 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 removed outlier: 3.586A pdb=" N ILE E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.898A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.648A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) 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 126 removed outlier: 3.894A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.691A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 210 removed outlier: 3.821A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 41 Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 128 through 150 removed outlier: 3.823A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 184 Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.563A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 128 through 147 Processing helix chain 'H' and resid 155 through 184 removed outlier: 3.785A pdb=" N ALA H 184 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.963A 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: 3.586A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 472 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 473 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 731 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 475 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.586A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 472 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 473 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 731 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 475 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 3.798A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.069A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 503 through 504 removed outlier: 3.761A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 721 " --> pdb=" O ILE B 504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.294A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 391 through 395 Processing sheet with id=AB1, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB2, first strand: chain 'C' and resid 447 through 450 Processing sheet with id=AB3, first strand: chain 'C' and resid 471 through 476 removed outlier: 9.873A pdb=" N ALA C 471 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 471 through 476 removed outlier: 9.873A pdb=" N ALA C 471 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.875A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 719 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 475 through 480 removed outlier: 7.222A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 646 through 648 removed outlier: 7.011A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.528A pdb=" N SER E 175 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AC1, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.816A pdb=" N LEU F 76 " --> pdb=" O CYS F 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AC3, first strand: chain 'H' and resid 82 through 84 1065 hydrogen bonds defined for protein. 3120 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: 3.00 Time building geometry restraints manager: 2.10 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: 3260 1.33 - 1.46: 5363 1.46 - 1.59: 9363 1.59 - 1.71: 16 1.71 - 1.84: 168 Bond restraints: 18170 Sorted by residual: bond pdb=" O12 POV C1004 " pdb=" P POV C1004 " 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 A1004 " pdb=" P POV A1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" O12 POV D1004 " pdb=" P POV D1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" O12 POV B1003 " pdb=" P POV B1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" O12 POV B1004 " pdb=" P POV B1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 18165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 24131 2.73 - 5.47: 316 5.47 - 8.20: 45 8.20 - 10.94: 6 10.94 - 13.67: 1 Bond angle restraints: 24499 Sorted by residual: angle pdb=" C GLN F 9 " pdb=" N MET F 10 " pdb=" CA MET F 10 " ideal model delta sigma weight residual 121.14 112.97 8.17 1.75e+00 3.27e-01 2.18e+01 angle pdb=" CB MET F 10 " pdb=" CG MET F 10 " pdb=" SD MET F 10 " ideal model delta sigma weight residual 112.70 126.37 -13.67 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N MET F 10 " pdb=" CA MET F 10 " pdb=" CB MET F 10 " ideal model delta sigma weight residual 110.40 117.46 -7.06 1.63e+00 3.76e-01 1.88e+01 angle pdb=" CA MET F 10 " pdb=" CB MET F 10 " pdb=" CG MET F 10 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CA ARG B 743 " pdb=" CB ARG B 743 " pdb=" CG ARG B 743 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 ... (remaining 24494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 10438 35.28 - 70.55: 177 70.55 - 105.83: 19 105.83 - 141.11: 21 141.11 - 176.39: 4 Dihedral angle restraints: 10659 sinusoidal: 4045 harmonic: 6614 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 93.00 155.35 -62.35 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual -86.00 -145.43 59.43 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 143.92 -50.92 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 10656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2509 0.075 - 0.151: 253 0.151 - 0.226: 20 0.226 - 0.302: 0 0.302 - 0.377: 1 Chirality restraints: 2783 Sorted by residual: chirality pdb=" CB ILE C 485 " pdb=" CA ILE C 485 " pdb=" CG1 ILE C 485 " pdb=" CG2 ILE C 485 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CG LEU F 136 " pdb=" CB LEU F 136 " pdb=" CD1 LEU F 136 " pdb=" CD2 LEU F 136 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR F 66 " pdb=" CA THR F 66 " pdb=" OG1 THR F 66 " pdb=" CG2 THR F 66 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2780 not shown) Planarity restraints: 2978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 83 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO F 84 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 84 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 84 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 9 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" CD GLN F 9 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLN F 9 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN F 9 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 520 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.042 5.00e-02 4.00e+02 ... (remaining 2975 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3261 2.77 - 3.30: 17178 3.30 - 3.84: 29004 3.84 - 4.37: 33647 4.37 - 4.90: 58343 Nonbonded interactions: 141433 Sorted by model distance: nonbonded pdb=" O GLY C 568 " pdb=" OG SER C 572 " model vdw 2.238 3.040 nonbonded pdb=" OE2 GLU B 524 " pdb=" OH TYR F 174 " model vdw 2.272 3.040 nonbonded pdb=" O VAL B 681 " pdb=" OH TYR B 700 " model vdw 2.273 3.040 nonbonded pdb=" O VAL D 681 " pdb=" OH TYR D 700 " model vdw 2.283 3.040 nonbonded pdb=" O ILE F 154 " pdb=" OG SER F 158 " model vdw 2.296 3.040 ... (remaining 141428 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 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 through 398 or resid 400 through 403 o \ r resid 405 through 407 or resid 412 through 414 or resid 416 through 422 or res \ id 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 through 4 \ 41 or (resid 443 and (name N or name CA or name C or name O or name CB )) or res \ id 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 461 or (res \ id 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 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 through 543 or \ (resid 565 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 6 through 581 or resid 583 through 629 or (resid 630 and (name N or name CA or n \ ame C or name O or name CB )) or resid 631 through 635 or (resid 637 through 640 \ and (name N or name CA or name C or name O or name CB )) or resid 641 through 6 \ 46 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 o \ r name O or name CB )) or resid 654 through 656 or (resid 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 663 or resid 665 thr \ ough 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) \ or resid 672 through 675 or (resid 676 and (name N or name CA or name C or name \ O or name CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 t \ hrough 690 or (resid 691 through 693 and (name N or name CA or name C or name O \ or name CB )) or resid 694 through 736 or resid 738 through 739 or resid 742 thr \ ough 749 or resid 751 through 753 or resid 755 through 759 or resid 761 through \ 771 or (resid 776 through 777 and (name N or name CA or name C or name O or name \ CB )) or resid 779 through 795 or resid 797 through 1003 or (resid 1004 and (na \ me C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or n \ ame O31 or name O32 or name P or name C310 or name C311 or name C312)) or resid \ 1005 or (resid 1006 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name O1 or name O2 )) or resid 1007)) 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 or (resid 410 \ through 411 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 16 through 418 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 or (resid 422 and (name N or name CA or name C or name O or n \ ame CB )) or resid 423 through 426 or resid 428 through 435 or resid 437 or resi \ d 440 or resid 442 or resid 444 through 445 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 452 or (resid 453 throug \ h 454 and (name N or name CA or name C or name O or name CB )) or (resid 456 thr \ ough 458 and (name N or name CA or name C or name O or name CB )) or resid 460 t \ hrough 470 or resid 472 through 473 or resid 475 or resid 477 through 486 or (re \ sid 487 and (name N or name CA or name C or name O or name CB )) or resid 488 th \ rough 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) \ or resid 506 through 507 or (resid 508 through 509 and (name N or name CA or na \ me C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA o \ r name C or name O or name CB )) or resid 512 through 585 or resid 587 through 6 \ 39 or (resid 641 through 644 and (name N or name CA or name C or name O or name \ CB )) or resid 645 through 650 or resid 653 or (resid 654 and (name N or name CA \ or name C or name O or name CB )) or resid 655 through 667 or resid 669 through \ 674 or resid 676 through 684 or (resid 685 and (name 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 through 695 or (resid 696 thr \ ough 697 and (name N or name CA or name C or name O or name CB )) or resid 698 t \ hrough 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 through 743 or resid 746 thr \ ough 753 or resid 755 through 757 or resid 759 through 763 or resid 765 through \ 768 or (resid 769 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 resi \ d 801 through 817 or resid 1001 through 1003 or (resid 1004 and (name C1 or name \ C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or n \ ame C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O \ 11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or na \ me O32 or name P or name C310 or name C311 or name C312)) or resid 1005 through \ 1006 or (resid 1007 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 )))) selection = (chain 'C' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 through 398 or resid 400 through 403 o \ r resid 405 through 407 or resid 412 through 414 or resid 416 through 422 or res \ id 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 through 4 \ 41 or (resid 443 and (name N or name CA or name C or name O or name CB )) or res \ id 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 461 or (res \ id 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 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 through 543 or \ (resid 565 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 6 through 581 or resid 583 through 629 or (resid 630 and (name N or name CA or n \ ame C or name O or name CB )) or resid 631 through 635 or (resid 637 through 640 \ and (name N or name CA or name C or name O or name CB )) or resid 641 through 6 \ 46 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 o \ r name O or name CB )) or resid 654 through 656 or (resid 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 663 or resid 665 thr \ ough 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) \ or resid 672 through 675 or (resid 676 and (name N or name CA or name C or name \ O or name CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 t \ hrough 690 or (resid 691 through 693 and (name N or name CA or name C or name O \ or name CB )) or resid 694 or (resid 695 and (name N or name CA or name C or nam \ e O or name CB )) or resid 696 through 710 or (resid 711 through 712 and (name N \ or name CA or name C or name O or name CB )) or resid 713 through 714 or (resid \ 715 and (name N or name CA or name C or name O or name CB )) or resid 716 throu \ gh 736 or resid 738 through 739 or resid 742 through 749 or resid 751 through 75 \ 3 or resid 755 through 759 or resid 761 through 771 or (resid 776 through 777 an \ d (name N or name CA or name C or name O or name CB )) or resid 779 through 795 \ or resid 797 through 1003 or (resid 1004 and (name C1 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C310 or name C311 or name C312)) or resid 1005 or (resid 1006 and (name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1 or \ name O2 )) or (resid 1007 and (name C1 or name C2 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 )))) 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 and (name N or name CA or name C or name O \ or name CB )) or resid 421 through 426 or resid 428 through 435 or resid 437 or \ resid 440 or resid 442 or resid 444 through 445 or (resid 447 through 449 and ( \ name N or name CA or name C or name O or name CB )) or resid 450 through 452 or \ (resid 453 through 454 and (name N or name CA or name C or name O or name CB )) \ or (resid 456 through 458 and (name N or name CA or name C or name O or name CB \ )) or resid 460 through 465 or (resid 466 and (name N or name CA or name C or na \ me O or name CB )) or resid 467 through 470 or resid 472 through 473 or resid 47 \ 5 or resid 477 through 486 or (resid 487 and (name N or name CA or name C or nam \ e O or name CB )) or resid 488 through 504 or (resid 505 and (name N or name CA \ or name C or name O or name CB )) or resid 506 through 507 or (resid 508 through \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 or (r \ esid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 t \ hrough 585 or resid 587 through 639 or resid 641 through 650 or resid 653 throug \ h 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 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 683 or ( \ resid 684 through 685 and (name N or name CA or name C or name O or name CB )) o \ r 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 through 694 or (resid 695 through 697 and (name N o \ r name CA or name C or name O or name CB )) or resid 698 through 714 or (resid 7 \ 15 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 through 743 or resid 746 through 753 or resid 755 \ through 757 or resid 759 through 763 or resid 765 through 768 or (resid 769 and \ (name N or name CA or name C or name O or name CB )) or resid 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 816 or ( \ resid 817 and (name N or name CA or name C or name O or name CB )) or resid 1001 \ through 1006 or (resid 1007 and (name C1 or name C2 or name C3 or name C4 or na \ me C5 or name C6 or name C7 or name C8 )))) } ncs_group { reference = (chain 'E' and (resid 4 through 57 or (resid 58 and (name N or name CA or name C \ or name O or name CB )) or resid 59 through 210)) selection = (chain 'F' and (resid 4 through 85 or (resid 86 through 91 and (name N or name C \ A or name C or name O or name CB )) or resid 92 through 210)) } ncs_group { reference = (chain 'G' and (resid 19 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 231)) selection = (chain 'H' and (resid 19 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 231)) } 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: 5.450 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.800 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 0.051 18182 Z= 0.234 Angle : 0.778 13.675 24523 Z= 0.396 Chirality : 0.047 0.377 2783 Planarity : 0.006 0.079 2978 Dihedral : 15.972 176.387 6411 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.61 (0.17), residues: 2272 helix: 0.83 (0.14), residues: 1280 sheet: -1.96 (0.43), residues: 134 loop : -2.06 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 656 TYR 0.029 0.001 TYR G 226 PHE 0.048 0.002 PHE G 165 TRP 0.044 0.002 TRP E 178 HIS 0.008 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (18170) covalent geometry : angle 0.77648 / 0.39 (24499) SS BOND : bond 0.00521 / 0.29 ( 12) SS BOND : angle 1.94386 / 1.19 ( 24) hydrogen bonds : bond 0.14440 / 9.93 ( 1058) hydrogen bonds : angle 5.80994 / 4.12 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 VAL cc_start: 0.8209 (p) cc_final: 0.7929 (m) REVERT: A 496 ILE cc_start: 0.8119 (mt) cc_final: 0.7864 (mt) REVERT: A 590 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7552 (mtp180) REVERT: A 640 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7089 (pt0) REVERT: A 804 LEU cc_start: 0.7031 (mt) cc_final: 0.6821 (mt) REVERT: B 404 PRO cc_start: 0.6187 (Cg_endo) cc_final: 0.5923 (Cg_exo) REVERT: B 469 TYR cc_start: 0.6512 (m-80) cc_final: 0.6278 (m-80) REVERT: B 527 MET cc_start: 0.6454 (mmm) cc_final: 0.5644 (ttp) REVERT: B 645 ILE cc_start: 0.7641 (mm) cc_final: 0.7244 (mt) REVERT: B 671 TRP cc_start: 0.8373 (t-100) cc_final: 0.7998 (t-100) REVERT: C 392 ILE cc_start: 0.7779 (mm) cc_final: 0.7499 (mm) REVERT: C 492 MET cc_start: 0.9134 (ttm) cc_final: 0.8838 (ttp) REVERT: C 499 MET cc_start: 0.8207 (ttt) cc_final: 0.7806 (ttm) REVERT: C 590 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7089 (mtm180) REVERT: C 623 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7397 (pt0) REVERT: C 666 MET cc_start: 0.6680 (mtm) cc_final: 0.6446 (mtp) REVERT: C 671 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7718 (ttpp) REVERT: C 730 ILE cc_start: 0.7811 (pt) cc_final: 0.7545 (pt) REVERT: D 594 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.7635 (mmt-90) REVERT: E 31 ASP cc_start: 0.7495 (m-30) cc_final: 0.6980 (m-30) REVERT: E 117 MET cc_start: 0.7116 (mmm) cc_final: 0.6884 (mtt) REVERT: E 196 LEU cc_start: 0.7286 (mm) cc_final: 0.7081 (mt) REVERT: F 9 GLN cc_start: 0.8349 (pp30) cc_final: 0.8136 (pp30) REVERT: F 80 ILE cc_start: 0.5930 (mm) cc_final: 0.5721 (pt) REVERT: F 106 ILE cc_start: 0.7608 (tp) cc_final: 0.7356 (tp) REVERT: F 114 LEU cc_start: 0.7319 (mm) cc_final: 0.7064 (mm) REVERT: G 37 ILE cc_start: 0.7282 (mm) cc_final: 0.7081 (mm) REVERT: G 106 PHE cc_start: 0.6316 (m-80) cc_final: 0.6046 (m-80) REVERT: G 229 ARG cc_start: 0.6991 (tmm160) cc_final: 0.6352 (ttm-80) REVERT: H 158 ILE cc_start: 0.7100 (mm) cc_final: 0.6840 (mm) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.1366 time to fit residues: 90.6740 Evaluate side-chains 338 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.190053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139968 restraints weight = 23954.400| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.47 r_work: 0.3521 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18182 Z= 0.119 Angle : 0.543 10.542 24523 Z= 0.283 Chirality : 0.040 0.253 2783 Planarity : 0.005 0.064 2978 Dihedral : 12.125 169.665 3012 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.55 % Allowed : 9.16 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.37 (0.18), residues: 2272 helix: 1.79 (0.15), residues: 1304 sheet: -2.06 (0.38), residues: 162 loop : -1.92 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 739 TYR 0.011 0.001 TYR A 707 PHE 0.022 0.001 PHE B 574 TRP 0.015 0.001 TRP E 178 HIS 0.019 0.002 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18170) covalent geometry : angle 0.54236 / 0.28 (24499) SS BOND : bond 0.00793 / 0.65 ( 12) SS BOND : angle 1.21312 / 0.72 ( 24) hydrogen bonds : bond 0.03737 / 2.49 ( 1058) hydrogen bonds : angle 4.11408 / 2.88 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 350 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8929 (mt) cc_final: 0.8705 (mt) REVERT: A 623 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7183 (mt-10) REVERT: A 640 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7451 (pt0) REVERT: A 804 LEU cc_start: 0.8146 (mt) cc_final: 0.7931 (mt) REVERT: B 503 MET cc_start: 0.8112 (ttt) cc_final: 0.7510 (ttt) REVERT: B 645 ILE cc_start: 0.7925 (mm) cc_final: 0.7512 (mt) REVERT: B 671 TRP cc_start: 0.8335 (t-100) cc_final: 0.8065 (t-100) REVERT: C 541 ARG cc_start: 0.7679 (mmt180) cc_final: 0.7310 (mmm160) REVERT: C 590 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8066 (mtm180) REVERT: D 594 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8011 (mmt180) REVERT: D 742 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7486 (tt) REVERT: E 97 PHE cc_start: 0.6943 (t80) cc_final: 0.6565 (t80) REVERT: F 80 ILE cc_start: 0.6642 (mm) cc_final: 0.6360 (pt) REVERT: F 192 MET cc_start: 0.8280 (mtp) cc_final: 0.7953 (tpp) REVERT: G 106 PHE cc_start: 0.6515 (m-80) cc_final: 0.6207 (m-80) REVERT: G 140 LEU cc_start: 0.7296 (mp) cc_final: 0.6972 (mp) REVERT: G 229 ARG cc_start: 0.7088 (tmm160) cc_final: 0.6503 (ttm-80) outliers start: 26 outliers final: 12 residues processed: 363 average time/residue: 0.1245 time to fit residues: 69.8650 Evaluate side-chains 339 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 326 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain G residue 89 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 69 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129675 restraints weight = 23525.703| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.74 r_work: 0.3343 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18182 Z= 0.203 Angle : 0.611 8.106 24523 Z= 0.320 Chirality : 0.043 0.215 2783 Planarity : 0.005 0.068 2978 Dihedral : 12.470 168.778 3012 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.44 % Allowed : 12.79 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.28 (0.18), residues: 2272 helix: 1.76 (0.15), residues: 1286 sheet: -1.72 (0.45), residues: 138 loop : -2.06 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 204 TYR 0.018 0.002 TYR C 669 PHE 0.037 0.002 PHE F 141 TRP 0.028 0.002 TRP F 178 HIS 0.010 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (18170) covalent geometry : angle 0.61017 / 0.32 (24499) SS BOND : bond 0.00428 / 0.33 ( 12) SS BOND : angle 1.16566 / 0.68 ( 24) hydrogen bonds : bond 0.04143 / 2.73 ( 1058) hydrogen bonds : angle 4.13684 / 2.89 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 640 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7471 (pt0) REVERT: A 804 LEU cc_start: 0.7971 (mt) cc_final: 0.7615 (mt) REVERT: B 420 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6474 (mtm-85) REVERT: B 469 TYR cc_start: 0.6848 (m-80) cc_final: 0.6503 (m-80) REVERT: B 519 ASP cc_start: 0.8413 (m-30) cc_final: 0.8164 (m-30) REVERT: B 645 ILE cc_start: 0.8052 (mm) cc_final: 0.7646 (mt) REVERT: C 519 TYR cc_start: 0.8593 (t80) cc_final: 0.8337 (t80) REVERT: C 590 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8059 (mtm180) REVERT: E 97 PHE cc_start: 0.6802 (t80) cc_final: 0.6312 (t80) REVERT: F 141 PHE cc_start: 0.8270 (m-80) cc_final: 0.7980 (m-80) REVERT: F 192 MET cc_start: 0.8248 (mtp) cc_final: 0.7863 (tpp) REVERT: G 106 PHE cc_start: 0.6558 (m-80) cc_final: 0.6114 (m-80) REVERT: G 129 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (mt) REVERT: G 229 ARG cc_start: 0.7054 (tmm160) cc_final: 0.6447 (ttm-80) outliers start: 41 outliers final: 25 residues processed: 333 average time/residue: 0.1292 time to fit residues: 66.2330 Evaluate side-chains 315 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 224 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 225 optimal weight: 0.3980 chunk 211 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 105 HIS H 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132479 restraints weight = 24086.948| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.83 r_work: 0.3401 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18182 Z= 0.157 Angle : 0.549 7.891 24523 Z= 0.289 Chirality : 0.041 0.183 2783 Planarity : 0.004 0.062 2978 Dihedral : 12.070 173.861 3012 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.26 % Allowed : 14.75 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.42 (0.18), residues: 2272 helix: 1.93 (0.15), residues: 1288 sheet: -2.05 (0.40), residues: 166 loop : -2.01 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.014 0.001 TYR C 669 PHE 0.031 0.002 PHE F 83 TRP 0.017 0.001 TRP F 178 HIS 0.010 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (18170) covalent geometry : angle 0.54889 / 0.29 (24499) SS BOND : bond 0.00574 / 0.47 ( 12) SS BOND : angle 0.98201 / 0.57 ( 24) hydrogen bonds : bond 0.03703 / 2.45 ( 1058) hydrogen bonds : angle 3.95115 / 2.76 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7538 (pt0) REVERT: A 804 LEU cc_start: 0.8174 (mt) cc_final: 0.7832 (mt) REVERT: B 469 TYR cc_start: 0.7000 (m-80) cc_final: 0.6593 (m-80) REVERT: B 519 ASP cc_start: 0.8295 (m-30) cc_final: 0.8055 (m-30) REVERT: B 645 ILE cc_start: 0.8070 (mm) cc_final: 0.7663 (mt) REVERT: C 541 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7416 (mmt180) REVERT: C 590 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8156 (mtm180) REVERT: D 627 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6741 (mm-30) REVERT: D 817 LYS cc_start: 0.7997 (mmtm) cc_final: 0.6908 (mtpt) REVERT: E 97 PHE cc_start: 0.6801 (t80) cc_final: 0.6274 (t80) REVERT: F 141 PHE cc_start: 0.8485 (m-80) cc_final: 0.8276 (m-80) REVERT: G 106 PHE cc_start: 0.6686 (m-80) cc_final: 0.6273 (m-80) REVERT: G 140 LEU cc_start: 0.7473 (mp) cc_final: 0.7181 (mp) REVERT: G 229 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6572 (ttm-80) outliers start: 38 outliers final: 23 residues processed: 330 average time/residue: 0.1267 time to fit residues: 64.2515 Evaluate side-chains 308 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 103 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 9 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 47 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.179545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127996 restraints weight = 23432.279| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.50 r_work: 0.3344 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18182 Z= 0.202 Angle : 0.608 10.002 24523 Z= 0.317 Chirality : 0.042 0.197 2783 Planarity : 0.004 0.064 2978 Dihedral : 12.477 172.847 3012 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.21 % Allowed : 15.70 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.29 (0.18), residues: 2272 helix: 1.80 (0.15), residues: 1294 sheet: -1.79 (0.41), residues: 168 loop : -2.11 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 739 TYR 0.024 0.002 TYR A 707 PHE 0.026 0.002 PHE F 83 TRP 0.024 0.002 TRP F 178 HIS 0.009 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (18170) covalent geometry : angle 0.60792 / 0.32 (24499) SS BOND : bond 0.00318 / 0.23 ( 12) SS BOND : angle 1.00935 / 0.59 ( 24) hydrogen bonds : bond 0.03982 / 2.62 ( 1058) hydrogen bonds : angle 4.07169 / 2.85 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 LEU cc_start: 0.8069 (mt) cc_final: 0.7722 (mt) REVERT: B 420 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6723 (mtm-85) REVERT: B 469 TYR cc_start: 0.6971 (m-80) cc_final: 0.6486 (m-80) REVERT: B 519 ASP cc_start: 0.8458 (m-30) cc_final: 0.8136 (m-30) REVERT: B 590 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: B 645 ILE cc_start: 0.8133 (mm) cc_final: 0.7731 (mt) REVERT: C 519 TYR cc_start: 0.8647 (t80) cc_final: 0.8434 (t80) REVERT: C 590 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8193 (mtm180) REVERT: D 490 ASP cc_start: 0.7679 (p0) cc_final: 0.7468 (p0) REVERT: E 97 PHE cc_start: 0.6751 (t80) cc_final: 0.6202 (t80) REVERT: F 141 PHE cc_start: 0.8478 (m-80) cc_final: 0.8154 (m-80) REVERT: G 106 PHE cc_start: 0.6603 (m-80) cc_final: 0.6281 (m-80) REVERT: G 229 ARG cc_start: 0.7096 (tmm160) cc_final: 0.6555 (ttm-80) REVERT: H 226 TYR cc_start: 0.7658 (t80) cc_final: 0.7449 (t80) outliers start: 54 outliers final: 35 residues processed: 336 average time/residue: 0.1308 time to fit residues: 67.4049 Evaluate side-chains 324 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 62 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132363 restraints weight = 23476.631| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.72 r_work: 0.3348 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18182 Z= 0.162 Angle : 0.611 21.388 24523 Z= 0.313 Chirality : 0.042 0.283 2783 Planarity : 0.004 0.064 2978 Dihedral : 12.198 167.695 3012 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.15 % Allowed : 16.48 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.36 (0.18), residues: 2272 helix: 1.89 (0.15), residues: 1294 sheet: -2.11 (0.37), residues: 194 loop : -2.04 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 684 TYR 0.025 0.001 TYR A 707 PHE 0.032 0.002 PHE F 83 TRP 0.013 0.001 TRP F 178 HIS 0.009 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (18170) covalent geometry : angle 0.60458 / 0.31 (24499) SS BOND : bond 0.00499 / 0.40 ( 12) SS BOND : angle 2.94365 / 1.94 ( 24) hydrogen bonds : bond 0.03809 / 2.54 ( 1058) hydrogen bonds : angle 4.01433 / 2.81 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: B 469 TYR cc_start: 0.6923 (m-80) cc_final: 0.6399 (m-80) REVERT: B 519 ASP cc_start: 0.8486 (m-30) cc_final: 0.8144 (m-30) REVERT: B 590 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6416 (m-30) REVERT: B 645 ILE cc_start: 0.8124 (mm) cc_final: 0.7720 (mt) REVERT: C 541 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7105 (mmt180) REVERT: C 590 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8209 (mtm180) REVERT: E 97 PHE cc_start: 0.6720 (t80) cc_final: 0.6196 (t80) REVERT: E 132 HIS cc_start: 0.4739 (OUTLIER) cc_final: 0.3009 (t70) REVERT: F 141 PHE cc_start: 0.8412 (m-80) cc_final: 0.8176 (m-80) REVERT: G 106 PHE cc_start: 0.6572 (m-80) cc_final: 0.6259 (m-80) REVERT: G 129 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7920 (mt) REVERT: G 140 LEU cc_start: 0.7422 (mm) cc_final: 0.7003 (mp) REVERT: G 229 ARG cc_start: 0.7074 (tmm160) cc_final: 0.6565 (ttm-80) REVERT: H 226 TYR cc_start: 0.7600 (t80) cc_final: 0.7371 (t80) outliers start: 53 outliers final: 36 residues processed: 327 average time/residue: 0.1290 time to fit residues: 64.8969 Evaluate side-chains 319 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 178 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 145 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130828 restraints weight = 23420.090| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.51 r_work: 0.3381 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18182 Z= 0.137 Angle : 0.583 18.036 24523 Z= 0.300 Chirality : 0.041 0.259 2783 Planarity : 0.004 0.061 2978 Dihedral : 11.528 126.626 3012 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.91 % Allowed : 17.25 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.52 (0.18), residues: 2272 helix: 2.01 (0.15), residues: 1294 sheet: -2.02 (0.37), residues: 186 loop : -1.97 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 684 TYR 0.027 0.001 TYR A 707 PHE 0.029 0.001 PHE F 83 TRP 0.013 0.001 TRP F 178 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18170) covalent geometry : angle 0.57779 / 0.30 (24499) SS BOND : bond 0.00451 / 0.37 ( 12) SS BOND : angle 2.54854 / 1.68 ( 24) hydrogen bonds : bond 0.03609 / 2.39 ( 1058) hydrogen bonds : angle 3.93852 / 2.76 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 804 LEU cc_start: 0.8028 (mt) cc_final: 0.7702 (mt) REVERT: B 420 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6705 (mtm-85) REVERT: B 469 TYR cc_start: 0.6990 (m-80) cc_final: 0.6494 (m-80) REVERT: B 519 ASP cc_start: 0.8372 (m-30) cc_final: 0.8008 (m-30) REVERT: B 590 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6335 (m-30) REVERT: B 645 ILE cc_start: 0.8079 (mm) cc_final: 0.7673 (mt) REVERT: C 392 ILE cc_start: 0.7994 (mm) cc_final: 0.7722 (mm) REVERT: C 541 ARG cc_start: 0.7539 (mmt180) cc_final: 0.7019 (mmp-170) REVERT: C 590 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8167 (mtm180) REVERT: D 627 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6737 (mm-30) REVERT: E 97 PHE cc_start: 0.6668 (t80) cc_final: 0.6137 (t80) REVERT: F 141 PHE cc_start: 0.8432 (m-80) cc_final: 0.8186 (m-80) REVERT: G 106 PHE cc_start: 0.6521 (m-80) cc_final: 0.6250 (m-80) REVERT: G 129 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (mt) REVERT: G 229 ARG cc_start: 0.7026 (tmm160) cc_final: 0.6559 (ttm-80) REVERT: H 226 TYR cc_start: 0.7598 (t80) cc_final: 0.7357 (t80) outliers start: 49 outliers final: 36 residues processed: 328 average time/residue: 0.1255 time to fit residues: 63.3476 Evaluate side-chains 322 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132940 restraints weight = 23553.881| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.57 r_work: 0.3363 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18182 Z= 0.160 Angle : 0.598 16.031 24523 Z= 0.307 Chirality : 0.042 0.232 2783 Planarity : 0.004 0.062 2978 Dihedral : 11.562 117.098 3012 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.74 % Allowed : 18.02 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.46 (0.18), residues: 2272 helix: 1.94 (0.15), residues: 1296 sheet: -2.04 (0.37), residues: 190 loop : -1.96 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 684 TYR 0.025 0.001 TYR A 707 PHE 0.026 0.001 PHE F 83 TRP 0.012 0.001 TRP F 178 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (18170) covalent geometry : angle 0.59412 / 0.31 (24499) SS BOND : bond 0.00441 / 0.35 ( 12) SS BOND : angle 2.15119 / 1.40 ( 24) hydrogen bonds : bond 0.03762 / 2.49 ( 1058) hydrogen bonds : angle 3.99772 / 2.79 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 739 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7392 (ttp80) REVERT: B 420 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6697 (mtm-85) REVERT: B 519 ASP cc_start: 0.8432 (m-30) cc_final: 0.8054 (m-30) REVERT: B 590 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6335 (m-30) REVERT: B 645 ILE cc_start: 0.8118 (mm) cc_final: 0.7721 (mt) REVERT: C 541 ARG cc_start: 0.7567 (mmt180) cc_final: 0.7178 (mmt180) REVERT: C 590 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8197 (mtm180) REVERT: D 627 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6723 (mm-30) REVERT: D 727 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8918 (mt) REVERT: D 817 LYS cc_start: 0.7972 (mmtm) cc_final: 0.6886 (tttm) REVERT: E 97 PHE cc_start: 0.6663 (t80) cc_final: 0.6121 (t80) REVERT: E 132 HIS cc_start: 0.4694 (OUTLIER) cc_final: 0.4052 (m90) REVERT: F 141 PHE cc_start: 0.8458 (m-80) cc_final: 0.8225 (m-80) REVERT: F 191 GLU cc_start: 0.7750 (mp0) cc_final: 0.7438 (mp0) REVERT: G 129 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (mt) REVERT: G 229 ARG cc_start: 0.7007 (tmm160) cc_final: 0.6544 (ttm-80) outliers start: 46 outliers final: 38 residues processed: 319 average time/residue: 0.1309 time to fit residues: 64.4040 Evaluate side-chains 322 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 100 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 152 optimal weight: 0.0020 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 0.0980 chunk 140 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.186434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136356 restraints weight = 23927.602| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.46 r_work: 0.3478 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18182 Z= 0.106 Angle : 0.558 14.683 24523 Z= 0.284 Chirality : 0.040 0.296 2783 Planarity : 0.004 0.061 2978 Dihedral : 10.697 98.043 3012 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.26 % Allowed : 18.98 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.75 (0.18), residues: 2272 helix: 2.21 (0.15), residues: 1298 sheet: -2.03 (0.37), residues: 190 loop : -1.88 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 684 TYR 0.027 0.001 TYR A 707 PHE 0.024 0.001 PHE F 83 TRP 0.015 0.001 TRP F 178 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (18170) covalent geometry : angle 0.55427 / 0.28 (24499) SS BOND : bond 0.00467 / 0.38 ( 12) SS BOND : angle 2.00387 / 1.30 ( 24) hydrogen bonds : bond 0.03352 / 2.23 ( 1058) hydrogen bonds : angle 3.79106 / 2.65 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7431 (mmp-170) REVERT: A 804 LEU cc_start: 0.8084 (mt) cc_final: 0.7828 (mt) REVERT: B 420 ARG cc_start: 0.7010 (mtm-85) cc_final: 0.6583 (mtm110) REVERT: B 427 ASP cc_start: 0.8029 (m-30) cc_final: 0.7794 (m-30) REVERT: B 645 ILE cc_start: 0.8035 (mm) cc_final: 0.7617 (mt) REVERT: C 590 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8204 (mtm180) REVERT: C 704 MET cc_start: 0.7692 (tpp) cc_final: 0.7468 (tpp) REVERT: D 817 LYS cc_start: 0.8073 (mmtm) cc_final: 0.6942 (tttm) REVERT: E 97 PHE cc_start: 0.6696 (t80) cc_final: 0.6161 (t80) REVERT: F 141 PHE cc_start: 0.8487 (m-80) cc_final: 0.8259 (m-80) REVERT: G 229 ARG cc_start: 0.6961 (tmm160) cc_final: 0.6531 (ttm-80) REVERT: H 45 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8033 (tt) outliers start: 38 outliers final: 30 residues processed: 331 average time/residue: 0.1353 time to fit residues: 68.3929 Evaluate side-chains 316 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 43 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 191 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.0470 chunk 121 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 0.0010 chunk 206 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136716 restraints weight = 23761.616| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.56 r_work: 0.3449 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18182 Z= 0.114 Angle : 0.569 13.717 24523 Z= 0.289 Chirality : 0.040 0.288 2783 Planarity : 0.004 0.062 2978 Dihedral : 10.478 95.350 3012 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.78 % Allowed : 20.46 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.79 (0.18), residues: 2272 helix: 2.22 (0.15), residues: 1294 sheet: -1.97 (0.41), residues: 152 loop : -1.84 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 684 TYR 0.022 0.001 TYR A 707 PHE 0.024 0.001 PHE F 83 TRP 0.033 0.001 TRP F 178 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (18170) covalent geometry : angle 0.56656 / 0.29 (24499) SS BOND : bond 0.00452 / 0.37 ( 12) SS BOND : angle 1.88790 / 1.22 ( 24) hydrogen bonds : bond 0.03390 / 2.26 ( 1058) hydrogen bonds : angle 3.83909 / 2.67 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.728 Fit side-chains REVERT: A 804 LEU cc_start: 0.8093 (mt) cc_final: 0.7848 (mt) REVERT: B 420 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6714 (mtm-85) REVERT: B 645 ILE cc_start: 0.8051 (mm) cc_final: 0.7628 (mt) REVERT: C 541 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7138 (mmt180) REVERT: C 590 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8234 (mtm180) REVERT: C 704 MET cc_start: 0.7730 (tpp) cc_final: 0.7487 (tpp) REVERT: D 817 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7029 (tttm) REVERT: E 97 PHE cc_start: 0.6701 (t80) cc_final: 0.6158 (t80) REVERT: F 141 PHE cc_start: 0.8509 (m-80) cc_final: 0.8272 (m-80) REVERT: F 191 GLU cc_start: 0.7793 (mp0) cc_final: 0.7059 (mp0) REVERT: G 229 ARG cc_start: 0.7005 (tmm160) cc_final: 0.6550 (ttm-80) REVERT: H 45 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8024 (tt) outliers start: 30 outliers final: 27 residues processed: 311 average time/residue: 0.1353 time to fit residues: 63.8853 Evaluate side-chains 306 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 213 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 0.0070 chunk 120 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.0050 chunk 183 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 overall best weight: 0.9816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 199 HIS F 199 HIS ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130047 restraints weight = 23607.469| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.60 r_work: 0.3376 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18182 Z= 0.141 Angle : 0.599 18.272 24523 Z= 0.304 Chirality : 0.041 0.272 2783 Planarity : 0.004 0.059 2978 Dihedral : 10.655 94.062 3012 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.08 % Allowed : 20.46 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.71 (0.18), residues: 2272 helix: 2.13 (0.15), residues: 1294 sheet: -2.02 (0.42), residues: 152 loop : -1.85 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 739 TYR 0.038 0.001 TYR F 156 PHE 0.034 0.001 PHE F 83 TRP 0.031 0.001 TRP F 178 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (18170) covalent geometry : angle 0.59671 / 0.30 (24499) SS BOND : bond 0.00480 / 0.39 ( 12) SS BOND : angle 1.85932 / 1.20 ( 24) hydrogen bonds : bond 0.03583 / 2.38 ( 1058) hydrogen bonds : angle 3.93257 / 2.74 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4965.80 seconds wall clock time: 85 minutes 33.72 seconds (5133.72 seconds total)