Starting phenix.real_space_refine on Fri Mar 6 18:50:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727.map" model { file = "/net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucb_20727/03_2026/6ucb_20727_trim.cif" } resolution = 3.28 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= 0.004 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 11048 2.51 5 N 2552 2.21 5 O 2894 1.98 5 F 12 1.80 5 H 15694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32324 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5781 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5778 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 5781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5781 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2121 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2145 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2121 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5778 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {'OLC': 1, 'PAM': 2, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 166 Unusual residues: {'CLR': 1, 'OLC': 3, 'PAM': 2, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {'OLC': 1, 'PAM': 2, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PAM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 138 Unusual residues: {'OLC': 3, 'PAM': 2, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.10, per 1000 atoms: 0.19 Number of scatterers: 32324 At special positions: 0 Unit cell: (122.59, 101.27, 147.108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 4 15.00 F 12 9.00 O 2894 8.00 N 2552 7.00 C 11048 6.00 H 15694 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 63.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 547 removed outlier: 3.500A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.787A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 660 removed outlier: 3.972A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.804A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 removed outlier: 4.251A pdb=" N LEU A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 823 removed outlier: 3.684A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.584A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.598A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 542 Processing helix chain 'B' and resid 599 through 627 removed outlier: 3.637A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.772A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.653A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 741 through 757 removed outlier: 4.532A pdb=" N ALA B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 824 removed outlier: 3.755A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 547 removed outlier: 3.500A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.786A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 660 removed outlier: 3.972A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.805A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.251A pdb=" N LEU C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 823 removed outlier: 3.683A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.658A pdb=" N CYS E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 67 removed outlier: 4.112A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.604A pdb=" N TYR E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.833A pdb=" N LEU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 93' Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.782A pdb=" N HIS E 107 " --> pdb=" O TRP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 158 removed outlier: 3.566A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 38 removed outlier: 3.619A pdb=" N CYS F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 68 through 85 removed outlier: 3.646A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 106 Proline residue: F 96 - end of helix removed outlier: 4.157A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 158 removed outlier: 4.261A pdb=" N SER F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.659A pdb=" N CYS G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 removed outlier: 4.112A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.603A pdb=" N TYR G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.832A pdb=" N LEU G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 92 " --> pdb=" O TRP G 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU G 93 " --> pdb=" O LEU G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 93' Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.781A pdb=" N HIS G 107 " --> pdb=" O TRP G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 158 removed outlier: 3.567A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 38 removed outlier: 3.619A pdb=" N CYS H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 68 through 85 removed outlier: 3.646A pdb=" N TYR H 72 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 106 Proline residue: H 96 - end of helix removed outlier: 4.157A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 4.261A pdb=" N SER H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR H 130 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.584A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.598A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 542 Processing helix chain 'D' and resid 599 through 627 removed outlier: 3.636A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.772A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.654A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 741 through 757 removed outlier: 4.532A pdb=" N ALA D 745 " --> pdb=" O SER D 741 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 824 removed outlier: 3.756A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.203A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.640A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.592A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 Processing sheet with id=AA7, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.367A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.515A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 4.014A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.204A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.638A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 500 through 501 Processing sheet with id=AB8, first strand: chain 'C' and resid 504 through 505 removed outlier: 3.591A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'D' and resid 395 through 396 removed outlier: 6.367A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AC4, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.515A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 646 through 648 removed outlier: 4.015A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2766 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: 7.78 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15642 1.04 - 1.25: 2190 1.25 - 1.45: 5236 1.45 - 1.65: 9454 1.65 - 1.86: 184 Bond restraints: 32706 Sorted by residual: bond pdb=" CAT ZK1 D 901 " pdb=" OAA ZK1 D 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" CAT ZK1 A 901 " pdb=" OAA ZK1 A 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" CAT ZK1 B 901 " pdb=" OAA ZK1 B 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 32701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 58019 2.15 - 4.30: 346 4.30 - 6.45: 74 6.45 - 8.61: 39 8.61 - 10.76: 19 Bond angle restraints: 58497 Sorted by residual: angle pdb=" C2 OLC B 903 " pdb=" C1 OLC B 903 " pdb=" O20 OLC B 903 " ideal model delta sigma weight residual 111.51 122.27 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C2 OLC B 902 " pdb=" C1 OLC B 902 " pdb=" O20 OLC B 902 " ideal model delta sigma weight residual 111.51 121.74 -10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2 OLC C 902 " pdb=" C1 OLC C 902 " pdb=" O20 OLC C 902 " ideal model delta sigma weight residual 111.51 121.58 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 OLC A 902 " pdb=" C1 OLC A 902 " pdb=" O20 OLC A 902 " ideal model delta sigma weight residual 111.51 121.48 -9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 OLC D 902 " pdb=" C1 OLC D 902 " pdb=" O20 OLC D 902 " ideal model delta sigma weight residual 111.51 121.47 -9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 58492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.94: 15270 30.94 - 61.87: 580 61.87 - 92.81: 12 92.81 - 123.75: 9 123.75 - 154.68: 4 Dihedral angle restraints: 15875 sinusoidal: 8497 harmonic: 7378 Sorted by residual: dihedral pdb=" C21 OLC B 903 " pdb=" C1 OLC B 903 " pdb=" O20 OLC B 903 " pdb=" O19 OLC B 903 " ideal model delta sinusoidal sigma weight residual -1.92 152.76 -154.68 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" O20 OLC B 903 " pdb=" C21 OLC B 903 " pdb=" C22 OLC B 903 " pdb=" O23 OLC B 903 " ideal model delta sinusoidal sigma weight residual 302.77 148.88 153.89 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C24 OLC B 903 " pdb=" C21 OLC B 903 " pdb=" C22 OLC B 903 " pdb=" O20 OLC B 903 " ideal model delta sinusoidal sigma weight residual -177.22 -29.19 -148.03 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 15872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2462 0.099 - 0.198: 76 0.198 - 0.297: 4 0.297 - 0.396: 0 0.396 - 0.495: 8 Chirality restraints: 2550 Sorted by residual: chirality pdb=" C22 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C24 OLC D 902 " pdb=" O23 OLC D 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.81 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C22 OLC D 903 " pdb=" C21 OLC D 903 " pdb=" C24 OLC D 903 " pdb=" O23 OLC D 903 " both_signs ideal model delta sigma weight residual False -2.31 -2.79 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C22 OLC B 903 " pdb=" C21 OLC B 903 " pdb=" C24 OLC B 903 " pdb=" O23 OLC B 903 " both_signs ideal model delta sigma weight residual False -2.31 -2.79 0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 2547 not shown) Planarity restraints: 4701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PAM D 905 " -0.265 2.00e-02 2.50e+03 2.29e-01 5.25e+02 pdb=" C11 PAM D 905 " 0.238 2.00e-02 2.50e+03 pdb=" C8 PAM D 905 " 0.218 2.00e-02 2.50e+03 pdb=" C9 PAM D 905 " -0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 903 " -0.223 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" C11 PAM A 903 " 0.219 2.00e-02 2.50e+03 pdb=" C8 PAM A 903 " 0.217 2.00e-02 2.50e+03 pdb=" C9 PAM A 903 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM C 903 " -0.291 2.00e-02 2.50e+03 2.17e-01 4.69e+02 pdb=" C11 PAM C 903 " 0.100 2.00e-02 2.50e+03 pdb=" C8 PAM C 903 " -0.097 2.00e-02 2.50e+03 pdb=" C9 PAM C 903 " 0.289 2.00e-02 2.50e+03 ... (remaining 4698 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1392 2.19 - 2.79: 64640 2.79 - 3.39: 86515 3.39 - 4.00: 111164 4.00 - 4.60: 175073 Nonbonded interactions: 438784 Sorted by model distance: nonbonded pdb="HH22 ARG B 545 " pdb=" O LYS G 66 " model vdw 1.584 2.450 nonbonded pdb="HH12 ARG B 485 " pdb=" OAA ZK1 B 901 " model vdw 1.601 2.450 nonbonded pdb=" HE ARG A 545 " pdb=" O LYS F 66 " model vdw 1.601 2.450 nonbonded pdb=" O LYS E 66 " pdb="HH22 ARG D 545 " model vdw 1.608 2.450 nonbonded pdb=" H LEU B 483 " pdb=" OE2 GLU C 755 " model vdw 1.652 2.450 ... (remaining 438779 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 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 674 or (resid 675 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 676 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 706 through 776 or (resid 784 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 785 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 786 through 902)) selection = (chain 'B' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r resid 395 through 539 or (resid 540 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid \ 541 through 637 or (resid 638 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 639 through 696 or (resid 697 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 700 through 902)) selection = (chain 'C' and (resid 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 674 or (resid 675 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 676 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 706 through 776 or (resid 784 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 785 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 786 through 902)) selection = (chain 'D' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r resid 395 through 539 or (resid 540 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid \ 541 through 637 or (resid 638 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 639 through 696 or (resid 697 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 700 through 902)) } ncs_group { reference = (chain 'E' and (resid 2 through 108 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or (resid 126 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) or \ (resid 128 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or resid 129 through 159 or resid 201)) selection = (chain 'F' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H o \ r name HA )) or resid 88 through 108 or resid 125 through 201)) selection = (chain 'G' and (resid 2 through 108 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or (resid 126 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) or \ (resid 128 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or resid 129 through 159 or resid 201)) selection = (chain 'H' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H o \ r name HA )) or resid 88 through 108 or resid 125 through 127 or (resid 128 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or resid 129 through 159 or resid 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.830 Find NCS groups from input model: 0.550 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.183 17016 Z= 0.441 Angle : 0.755 10.757 22950 Z= 0.328 Chirality : 0.047 0.495 2550 Planarity : 0.014 0.229 2744 Dihedral : 14.691 154.683 6390 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -3.14 (0.16), residues: 1996 helix: -1.18 (0.12), residues: 1242 sheet: -2.33 (0.50), residues: 104 loop : -3.72 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 545 TYR 0.013 0.001 TYR E 151 PHE 0.015 0.001 PHE D 531 TRP 0.007 0.001 TRP A 606 HIS 0.003 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00906 (17012) covalent geometry : angle 0.75521 (22942) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.23997 ( 8) hydrogen bonds : bond 0.13280 ( 950) hydrogen bonds : angle 5.25538 ( 2766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 450 TYR cc_start: 0.7158 (m-80) cc_final: 0.6732 (m-80) REVERT: E 100 TYR cc_start: 0.7138 (t80) cc_final: 0.6935 (t80) REVERT: E 134 GLU cc_start: 0.6324 (pt0) cc_final: 0.5918 (tt0) REVERT: F 66 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7685 (mtmt) REVERT: F 81 MET cc_start: 0.7199 (ttm) cc_final: 0.6601 (ttp) REVERT: F 138 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8485 (ttmt) REVERT: H 66 LYS cc_start: 0.7461 (mtpt) cc_final: 0.7066 (mtpt) REVERT: H 154 ILE cc_start: 0.7658 (mm) cc_final: 0.7414 (mm) REVERT: D 450 TYR cc_start: 0.7131 (m-80) cc_final: 0.6703 (m-80) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.3335 time to fit residues: 181.4995 Evaluate side-chains 221 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 791 ASN B 709 ASN B 791 ASN C 764 ASN C 791 ASN F 94 ASN H 94 ASN D 709 ASN D 791 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129178 restraints weight = 68655.432| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.38 r_work: 0.3334 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17016 Z= 0.164 Angle : 0.532 8.822 22950 Z= 0.280 Chirality : 0.038 0.146 2550 Planarity : 0.004 0.043 2744 Dihedral : 12.819 155.113 2912 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 0.60 % Allowed : 8.93 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -1.38 (0.18), residues: 1996 helix: 0.25 (0.14), residues: 1252 sheet: -2.05 (0.53), residues: 104 loop : -3.08 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.019 0.001 TYR H 155 PHE 0.023 0.002 PHE G 62 TRP 0.007 0.001 TRP C 606 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00381 (17012) covalent geometry : angle 0.53223 (22942) SS BOND : bond 0.00404 ( 4) SS BOND : angle 0.16640 ( 8) hydrogen bonds : bond 0.03898 ( 950) hydrogen bonds : angle 4.32593 ( 2766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 LEU cc_start: 0.6725 (mm) cc_final: 0.6215 (mm) REVERT: E 100 TYR cc_start: 0.6983 (t80) cc_final: 0.6691 (t80) REVERT: E 134 GLU cc_start: 0.5997 (pt0) cc_final: 0.5528 (tt0) REVERT: F 103 TRP cc_start: 0.6538 (t-100) cc_final: 0.5703 (t60) REVERT: F 138 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8546 (ttmt) REVERT: F 154 ILE cc_start: 0.7744 (mm) cc_final: 0.7447 (mm) REVERT: G 134 GLU cc_start: 0.6083 (pt0) cc_final: 0.5860 (tt0) REVERT: H 154 ILE cc_start: 0.7750 (mm) cc_final: 0.7510 (mm) REVERT: D 401 LEU cc_start: 0.6717 (mm) cc_final: 0.6205 (mm) outliers start: 10 outliers final: 6 residues processed: 248 average time/residue: 0.2607 time to fit residues: 100.1303 Evaluate side-chains 220 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 214 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN F 94 ASN H 94 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117016 restraints weight = 70567.142| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.29 r_work: 0.3280 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17016 Z= 0.174 Angle : 0.511 4.882 22950 Z= 0.276 Chirality : 0.038 0.140 2550 Planarity : 0.004 0.037 2744 Dihedral : 11.686 167.137 2912 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.66 % Allowed : 11.16 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.73 (0.19), residues: 1996 helix: 0.81 (0.15), residues: 1240 sheet: -2.26 (0.47), residues: 128 loop : -2.75 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 684 TYR 0.019 0.001 TYR F 155 PHE 0.022 0.002 PHE B 531 TRP 0.007 0.001 TRP F 103 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00410 (17012) covalent geometry : angle 0.51071 (22942) SS BOND : bond 0.00502 ( 4) SS BOND : angle 0.29505 ( 8) hydrogen bonds : bond 0.03938 ( 950) hydrogen bonds : angle 4.14055 ( 2766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 134 GLU cc_start: 0.5960 (pt0) cc_final: 0.5623 (tt0) REVERT: F 103 TRP cc_start: 0.6729 (t-100) cc_final: 0.5779 (t60) REVERT: F 138 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8543 (tttt) REVERT: F 154 ILE cc_start: 0.7713 (mm) cc_final: 0.7423 (mm) REVERT: H 3 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: H 21 ILE cc_start: 0.8799 (mt) cc_final: 0.8511 (pt) REVERT: H 143 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7975 (mt) REVERT: H 154 ILE cc_start: 0.7777 (mm) cc_final: 0.7508 (mm) outliers start: 11 outliers final: 9 residues processed: 231 average time/residue: 0.2569 time to fit residues: 91.4895 Evaluate side-chains 215 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118032 restraints weight = 70509.240| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.08 r_work: 0.3259 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17016 Z= 0.169 Angle : 0.495 4.566 22950 Z= 0.267 Chirality : 0.038 0.138 2550 Planarity : 0.004 0.037 2744 Dihedral : 11.060 158.061 2912 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.60 % Allowed : 12.30 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.44 (0.19), residues: 1996 helix: 1.03 (0.15), residues: 1246 sheet: -2.13 (0.48), residues: 122 loop : -2.65 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 545 TYR 0.018 0.001 TYR H 155 PHE 0.022 0.002 PHE B 531 TRP 0.007 0.001 TRP F 103 HIS 0.004 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (17012) covalent geometry : angle 0.49501 (22942) SS BOND : bond 0.00535 ( 4) SS BOND : angle 0.39503 ( 8) hydrogen bonds : bond 0.03692 ( 950) hydrogen bonds : angle 4.03660 ( 2766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 134 GLU cc_start: 0.6077 (pt0) cc_final: 0.5721 (tt0) REVERT: F 103 TRP cc_start: 0.6841 (t-100) cc_final: 0.5890 (t60) REVERT: H 3 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: H 21 ILE cc_start: 0.8808 (mt) cc_final: 0.8502 (pt) REVERT: H 134 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7762 (tt0) REVERT: H 154 ILE cc_start: 0.7972 (mm) cc_final: 0.7711 (mm) REVERT: D 534 ILE cc_start: 0.8886 (pt) cc_final: 0.8646 (mt) outliers start: 10 outliers final: 6 residues processed: 232 average time/residue: 0.2462 time to fit residues: 89.8130 Evaluate side-chains 211 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 165 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 186 optimal weight: 4.9990 overall best weight: 1.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120786 restraints weight = 70890.477| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.22 r_work: 0.3179 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17016 Z= 0.167 Angle : 0.491 4.855 22950 Z= 0.264 Chirality : 0.038 0.139 2550 Planarity : 0.004 0.047 2744 Dihedral : 10.327 109.364 2912 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 1.03 % Allowed : 13.09 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1996 helix: 1.18 (0.15), residues: 1246 sheet: -2.08 (0.47), residues: 122 loop : -2.52 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 104 TYR 0.018 0.001 TYR F 155 PHE 0.023 0.002 PHE B 531 TRP 0.006 0.001 TRP F 103 HIS 0.005 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (17012) covalent geometry : angle 0.49119 (22942) SS BOND : bond 0.00496 ( 4) SS BOND : angle 0.30468 ( 8) hydrogen bonds : bond 0.03659 ( 950) hydrogen bonds : angle 3.99151 ( 2766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 GLU cc_start: 0.8166 (pm20) cc_final: 0.7834 (pm20) REVERT: C 670 MET cc_start: 0.8967 (mtt) cc_final: 0.8721 (mtm) REVERT: E 33 GLU cc_start: 0.5478 (mm-30) cc_final: 0.5186 (mm-30) REVERT: F 103 TRP cc_start: 0.6843 (t-100) cc_final: 0.5920 (t60) REVERT: F 131 CYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7002 (t) REVERT: F 154 ILE cc_start: 0.7865 (mm) cc_final: 0.7655 (mm) REVERT: H 3 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: H 154 ILE cc_start: 0.7809 (mm) cc_final: 0.7578 (mm) REVERT: D 534 ILE cc_start: 0.8861 (pt) cc_final: 0.8613 (mt) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.2305 time to fit residues: 81.6229 Evaluate side-chains 212 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 135 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114692 restraints weight = 71970.576| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.22 r_work: 0.3267 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17016 Z= 0.163 Angle : 0.486 4.877 22950 Z= 0.261 Chirality : 0.038 0.135 2550 Planarity : 0.003 0.040 2744 Dihedral : 10.010 109.378 2912 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 0.90 % Allowed : 13.93 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1996 helix: 1.31 (0.15), residues: 1244 sheet: -2.04 (0.46), residues: 122 loop : -2.37 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 628 TYR 0.015 0.001 TYR H 155 PHE 0.022 0.002 PHE D 531 TRP 0.006 0.001 TRP F 103 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00381 (17012) covalent geometry : angle 0.48560 (22942) SS BOND : bond 0.00674 ( 4) SS BOND : angle 0.34788 ( 8) hydrogen bonds : bond 0.03585 ( 950) hydrogen bonds : angle 3.93969 ( 2766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 637 GLU cc_start: 0.8037 (pm20) cc_final: 0.7818 (pm20) REVERT: C 670 MET cc_start: 0.8935 (mtt) cc_final: 0.8675 (mtm) REVERT: E 33 GLU cc_start: 0.5562 (mm-30) cc_final: 0.5238 (mm-30) REVERT: F 103 TRP cc_start: 0.6786 (t-100) cc_final: 0.5906 (t60) REVERT: F 131 CYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7056 (t) REVERT: H 3 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: H 81 MET cc_start: 0.8505 (ttp) cc_final: 0.7970 (ttp) REVERT: D 534 ILE cc_start: 0.8832 (pt) cc_final: 0.8572 (mt) outliers start: 15 outliers final: 13 residues processed: 222 average time/residue: 0.2381 time to fit residues: 85.6671 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114528 restraints weight = 72265.985| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.24 r_work: 0.3264 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17016 Z= 0.150 Angle : 0.475 4.880 22950 Z= 0.255 Chirality : 0.037 0.134 2550 Planarity : 0.003 0.042 2744 Dihedral : 9.775 108.744 2912 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 1.03 % Allowed : 14.72 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.10 (0.19), residues: 1996 helix: 1.39 (0.15), residues: 1244 sheet: -2.00 (0.46), residues: 122 loop : -2.27 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 485 TYR 0.011 0.001 TYR H 155 PHE 0.021 0.001 PHE D 531 TRP 0.006 0.001 TRP F 26 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00350 (17012) covalent geometry : angle 0.47536 (22942) SS BOND : bond 0.00493 ( 4) SS BOND : angle 0.31880 ( 8) hydrogen bonds : bond 0.03512 ( 950) hydrogen bonds : angle 3.88750 ( 2766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 637 GLU cc_start: 0.8029 (pm20) cc_final: 0.7791 (pm20) REVERT: C 670 MET cc_start: 0.8992 (mtt) cc_final: 0.8753 (mtm) REVERT: E 33 GLU cc_start: 0.5478 (mm-30) cc_final: 0.5140 (mm-30) REVERT: F 103 TRP cc_start: 0.6810 (t-100) cc_final: 0.5964 (t60) REVERT: F 131 CYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7051 (t) REVERT: H 3 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: H 81 MET cc_start: 0.8513 (ttp) cc_final: 0.7994 (ttp) REVERT: H 155 TYR cc_start: 0.6755 (m-80) cc_final: 0.6494 (m-80) REVERT: D 534 ILE cc_start: 0.8823 (pt) cc_final: 0.8566 (mt) outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 0.2592 time to fit residues: 88.6499 Evaluate side-chains 210 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113953 restraints weight = 72050.070| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.22 r_work: 0.3255 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17016 Z= 0.169 Angle : 0.486 5.186 22950 Z= 0.262 Chirality : 0.038 0.136 2550 Planarity : 0.003 0.040 2744 Dihedral : 9.799 109.494 2912 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.45 % Allowed : 14.78 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.10 (0.19), residues: 1996 helix: 1.36 (0.15), residues: 1246 sheet: -1.95 (0.44), residues: 132 loop : -2.21 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 628 TYR 0.008 0.001 TYR F 105 PHE 0.022 0.002 PHE D 531 TRP 0.007 0.001 TRP F 103 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00398 (17012) covalent geometry : angle 0.48652 (22942) SS BOND : bond 0.00490 ( 4) SS BOND : angle 0.27994 ( 8) hydrogen bonds : bond 0.03557 ( 950) hydrogen bonds : angle 3.90443 ( 2766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.060 Fit side-chains REVERT: C 670 MET cc_start: 0.9006 (mtt) cc_final: 0.8722 (mtm) REVERT: F 103 TRP cc_start: 0.6786 (t-100) cc_final: 0.6002 (t60) REVERT: F 131 CYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7160 (t) REVERT: H 3 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: H 81 MET cc_start: 0.8545 (ttp) cc_final: 0.8023 (ttp) REVERT: H 148 TYR cc_start: 0.8679 (t80) cc_final: 0.8463 (t80) REVERT: H 155 TYR cc_start: 0.6671 (m-80) cc_final: 0.6436 (m-80) REVERT: D 534 ILE cc_start: 0.8834 (pt) cc_final: 0.8573 (mt) outliers start: 24 outliers final: 21 residues processed: 209 average time/residue: 0.2553 time to fit residues: 84.9847 Evaluate side-chains 215 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114248 restraints weight = 72147.645| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.23 r_work: 0.3259 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17016 Z= 0.154 Angle : 0.476 4.878 22950 Z= 0.256 Chirality : 0.037 0.134 2550 Planarity : 0.003 0.041 2744 Dihedral : 9.601 109.061 2912 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.33 % Allowed : 15.32 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.20 (0.19), residues: 1996 helix: 1.45 (0.15), residues: 1244 sheet: -1.88 (0.45), residues: 122 loop : -2.17 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 65 TYR 0.008 0.001 TYR F 105 PHE 0.022 0.001 PHE D 531 TRP 0.007 0.001 TRP F 26 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00359 (17012) covalent geometry : angle 0.47630 (22942) SS BOND : bond 0.00439 ( 4) SS BOND : angle 0.26753 ( 8) hydrogen bonds : bond 0.03491 ( 950) hydrogen bonds : angle 3.88496 ( 2766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.886 Fit side-chains REVERT: E 33 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5208 (mm-30) REVERT: F 81 MET cc_start: 0.8513 (ttp) cc_final: 0.7983 (ttp) REVERT: F 103 TRP cc_start: 0.6765 (t-100) cc_final: 0.5993 (t60) REVERT: F 131 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7125 (t) REVERT: H 3 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: H 81 MET cc_start: 0.8536 (ttp) cc_final: 0.8012 (ttp) REVERT: D 534 ILE cc_start: 0.8813 (pt) cc_final: 0.8556 (mt) outliers start: 22 outliers final: 18 residues processed: 206 average time/residue: 0.2736 time to fit residues: 88.5104 Evaluate side-chains 212 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN C 791 ASN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.148702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113564 restraints weight = 71809.007| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.18 r_work: 0.3249 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17016 Z= 0.178 Angle : 0.497 5.260 22950 Z= 0.268 Chirality : 0.038 0.138 2550 Planarity : 0.004 0.039 2744 Dihedral : 9.726 109.922 2912 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 1.39 % Allowed : 15.74 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.13 (0.19), residues: 1996 helix: 1.37 (0.15), residues: 1244 sheet: -1.86 (0.44), residues: 132 loop : -2.19 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 628 TYR 0.009 0.001 TYR C 647 PHE 0.024 0.002 PHE D 531 TRP 0.008 0.001 TRP F 103 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00420 (17012) covalent geometry : angle 0.49728 (22942) SS BOND : bond 0.00492 ( 4) SS BOND : angle 0.23611 ( 8) hydrogen bonds : bond 0.03614 ( 950) hydrogen bonds : angle 3.93328 ( 2766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 81 MET cc_start: 0.8740 (ttp) cc_final: 0.8244 (ttp) REVERT: F 103 TRP cc_start: 0.6977 (t-100) cc_final: 0.6130 (t60) REVERT: F 131 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7234 (t) REVERT: H 81 MET cc_start: 0.8717 (ttp) cc_final: 0.8243 (ttp) REVERT: H 148 TYR cc_start: 0.8753 (t80) cc_final: 0.8514 (t80) REVERT: D 534 ILE cc_start: 0.8884 (pt) cc_final: 0.8622 (mt) outliers start: 23 outliers final: 22 residues processed: 211 average time/residue: 0.2619 time to fit residues: 87.3370 Evaluate side-chains 218 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111944 restraints weight = 72890.694| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.24 r_work: 0.3230 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17016 Z= 0.215 Angle : 0.524 5.523 22950 Z= 0.283 Chirality : 0.039 0.146 2550 Planarity : 0.004 0.041 2744 Dihedral : 9.994 111.004 2912 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 1.63 % Allowed : 15.80 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.02 (0.19), residues: 1996 helix: 1.25 (0.15), residues: 1242 sheet: -1.83 (0.45), residues: 122 loop : -2.24 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.012 0.001 TYR H 155 PHE 0.027 0.002 PHE D 531 TRP 0.009 0.001 TRP F 103 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00509 (17012) covalent geometry : angle 0.52423 (22942) SS BOND : bond 0.00687 ( 4) SS BOND : angle 0.41553 ( 8) hydrogen bonds : bond 0.03780 ( 950) hydrogen bonds : angle 4.02379 ( 2766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7511.94 seconds wall clock time: 128 minutes 24.80 seconds (7704.80 seconds total)