Starting phenix.real_space_refine on Mon Sep 14 19:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.map" model { file = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ugm_20765/09_2026/6ugm_20765.cif" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11933 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 75 5.16 5 C 14001 2.51 5 N 4215 2.21 5 O 5025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23609 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 793 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2365 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1490 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Chain: "N" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3273 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "X" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 604 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Chain: "L" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3128 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "P" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 329 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15799 SG CYS M 988 102.405 78.131 52.399 1.00113.65 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET R 4 " occ=0.84 ... (6 atoms not shown) pdb=" CE MET R 4 " occ=0.84 residue: pdb="ZN ZN M1102 " occ=0.41 Time building chain proxies: 4.01, per 1000 atoms: 0.17 Number of scatterers: 23609 At special positions: 0 Unit cell: (174.24, 135.168, 141.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 75 16.00 P 292 15.00 O 5025 8.00 N 4215 7.00 C 14001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 623.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M1102 " pdb="ZN ZN M1102 " - pdb=" SG CYS M 988 " 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 29 sheets defined 31.7% alpha, 13.1% beta 132 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.131A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.671A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.892A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.827A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.638A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.615A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.530A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.728A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.694A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.765A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.590A pdb=" N GLY C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.794A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.010A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.513A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.918A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.927A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.700A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.547A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.597A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.895A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.503A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 77 removed outlier: 3.670A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.694A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.765A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.589A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.795A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.500A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 74 removed outlier: 3.975A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.841A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.705A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 732 removed outlier: 3.670A pdb=" N GLN M 731 " --> pdb=" O GLN M 727 " (cutoff:3.500A) Processing helix chain 'M' and resid 738 through 744 removed outlier: 3.738A pdb=" N ASN M 743 " --> pdb=" O GLN M 739 " (cutoff:3.500A) Processing helix chain 'M' and resid 894 through 908 removed outlier: 3.515A pdb=" N MET M 899 " --> pdb=" O PRO M 895 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS M 902 " --> pdb=" O GLU M 898 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR M 904 " --> pdb=" O ARG M 900 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE M 905 " --> pdb=" O GLU M 901 " (cutoff:3.500A) Processing helix chain 'M' and resid 931 through 935 removed outlier: 4.044A pdb=" N ILE M 935 " --> pdb=" O ALA M 932 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 8 removed outlier: 3.699A pdb=" N GLN N 7 " --> pdb=" O ASN N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 359 removed outlier: 3.709A pdb=" N ALA N 358 " --> pdb=" O LYS N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 376 through 380 removed outlier: 3.621A pdb=" N PHE N 379 " --> pdb=" O GLU N 376 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 433 removed outlier: 4.118A pdb=" N GLN N 432 " --> pdb=" O ILE N 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 199 through 211 removed outlier: 3.736A pdb=" N GLU X 207 " --> pdb=" O ASP X 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR X 209 " --> pdb=" O VAL X 205 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL X 210 " --> pdb=" O ILE X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 218 Processing helix chain 'X' and resid 219 through 224 Proline residue: X 222 - end of helix No H-bonds generated for 'chain 'X' and resid 219 through 224' Processing helix chain 'X' and resid 296 through 300 Processing helix chain 'X' and resid 303 through 317 removed outlier: 4.216A pdb=" N ARG X 310 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG X 311 " --> pdb=" O ASN X 307 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU X 312 " --> pdb=" O VAL X 308 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU X 314 " --> pdb=" O ARG X 310 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU X 315 " --> pdb=" O ARG X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 324 Processing helix chain 'L' and resid 194 through 209 removed outlier: 3.829A pdb=" N GLN L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP L 204 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS L 208 " --> pdb=" O ASP L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 238 removed outlier: 3.786A pdb=" N LEU L 235 " --> pdb=" O PHE L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 398 removed outlier: 4.031A pdb=" N ILE L 386 " --> pdb=" O THR L 382 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE L 395 " --> pdb=" O ILE L 391 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 92 through 94 No H-bonds generated for 'chain 'O' and resid 92 through 94' Processing helix chain 'O' and resid 97 through 104 removed outlier: 3.519A pdb=" N GLU O 101 " --> pdb=" O LYS O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 126 removed outlier: 3.501A pdb=" N LEU O 118 " --> pdb=" O PRO O 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE O 123 " --> pdb=" O GLY O 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'P' and resid 89 through 93 removed outlier: 3.918A pdb=" N ASN P 92 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 104 removed outlier: 3.620A pdb=" N LEU P 99 " --> pdb=" O VAL P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.307A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.602A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.384A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 22 removed outlier: 6.810A pdb=" N LEU K 323 " --> pdb=" O ASP K 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 34 through 36 removed outlier: 3.747A pdb=" N ILE K 43 " --> pdb=" O TYR K 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 74 through 77 removed outlier: 3.889A pdb=" N SER K 88 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR K 92 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL K 93 " --> pdb=" O ARG K 105 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG K 105 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE K 95 " --> pdb=" O ILE K 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 124 through 129 removed outlier: 3.914A pdb=" N LEU K 125 " --> pdb=" O TRP K 137 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP K 137 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 127 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 135 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER K 133 " --> pdb=" O SER K 129 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS K 146 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS K 138 " --> pdb=" O ALA K 144 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA K 144 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 155 through 159 removed outlier: 3.556A pdb=" N SER K 157 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER K 169 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 168 " --> pdb=" O PHE K 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG K 178 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP K 181 " --> pdb=" O CYS K 187 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS K 187 " --> pdb=" O ASP K 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 206 through 211 removed outlier: 3.549A pdb=" N LEU K 229 " --> pdb=" O ARG K 239 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG K 239 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU K 231 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL K 237 " --> pdb=" O GLU K 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 258 through 260 Processing sheet with id=AB3, first strand: chain 'K' and resid 305 through 306 removed outlier: 3.880A pdb=" N SER K 306 " --> pdb=" O ALA K 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 861 through 864 Processing sheet with id=AB5, first strand: chain 'M' and resid 885 through 887 removed outlier: 3.640A pdb=" N ILE M 885 " --> pdb=" O ILE M 958 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE M 956 " --> pdb=" O TYR M 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 892 through 893 Processing sheet with id=AB7, first strand: chain 'N' and resid 19 through 24 removed outlier: 5.161A pdb=" N LEU N 20 " --> pdb=" O SER N 349 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER N 349 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS N 22 " --> pdb=" O MET N 347 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG N 334 " --> pdb=" O ASN N 329 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN N 329 " --> pdb=" O ARG N 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 30 through 35 removed outlier: 6.404A pdb=" N GLY N 45 " --> pdb=" O VAL N 31 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL N 33 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA N 43 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE N 35 " --> pdb=" O TYR N 41 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR N 41 " --> pdb=" O PHE N 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 76 through 81 removed outlier: 7.029A pdb=" N LEU N 99 " --> pdb=" O PHE N 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 118 through 123 removed outlier: 4.405A pdb=" N SER N 120 " --> pdb=" O THR N 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'N' and resid 169 through 174 removed outlier: 3.689A pdb=" N VAL N 171 " --> pdb=" O GLY N 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 221 through 224 removed outlier: 3.539A pdb=" N GLN N 221 " --> pdb=" O ASN N 234 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE N 240 " --> pdb=" O LYS N 267 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS N 267 " --> pdb=" O ILE N 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN N 242 " --> pdb=" O GLU N 265 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU N 263 " --> pdb=" O GLN N 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 246 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 261 " --> pdb=" O ILE N 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 277 through 282 removed outlier: 6.707A pdb=" N SER N 293 " --> pdb=" O ASN N 278 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE N 280 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL N 291 " --> pdb=" O ILE N 280 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE N 282 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR N 289 " --> pdb=" O PHE N 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA N 292 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 302 " --> pdb=" O LEU N 316 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG N 314 " --> pdb=" O LEU N 304 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU N 306 " --> pdb=" O LEU N 312 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU N 312 " --> pdb=" O GLU N 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 52 through 55 removed outlier: 3.616A pdb=" N MET L 53 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER L 261 " --> pdb=" O MET L 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 55 " --> pdb=" O TYR L 259 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 249 " --> pdb=" O GLU L 260 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC8, first strand: chain 'L' and resid 88 through 89 removed outlier: 4.121A pdb=" N ALA L 362 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU L 122 " --> pdb=" O ILE L 365 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 119 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP L 121 " --> pdb=" O PHE L 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP L 184 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU L 291 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 105 through 114 removed outlier: 6.100A pdb=" N VAL L 112 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR L 350 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS L 133 " --> pdb=" O PHE L 357 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 165 through 167 Processing sheet with id=AD2, first strand: chain 'L' and resid 271 through 272 492 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 324 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3940 1.32 - 1.45: 7722 1.45 - 1.57: 12302 1.57 - 1.69: 582 1.69 - 1.82: 114 Bond restraints: 24660 Sorted by residual: bond pdb=" C LEU K 302 " pdb=" N ILE K 303 " ideal model delta sigma weight residual 1.334 1.227 0.106 1.26e-02 6.30e+03 7.12e+01 bond pdb=" N PRO O 114 " pdb=" CD PRO O 114 " ideal model delta sigma weight residual 1.473 1.560 -0.087 1.40e-02 5.10e+03 3.84e+01 bond pdb=" C THR M 754 " pdb=" N THR M 755 " ideal model delta sigma weight residual 1.334 1.260 0.074 1.38e-02 5.25e+03 2.87e+01 bond pdb=" C GLN M 894 " pdb=" N PRO M 895 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.20e-02 6.94e+03 2.57e+01 bond pdb=" C SER M 994 " pdb=" N CYS M 995 " ideal model delta sigma weight residual 1.329 1.267 0.063 1.25e-02 6.40e+03 2.53e+01 ... (remaining 24655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 34378 5.87 - 11.74: 184 11.74 - 17.61: 13 17.61 - 23.48: 7 23.48 - 29.35: 2 Bond angle restraints: 34584 Sorted by residual: angle pdb=" N LYS L 376 " pdb=" CA LYS L 376 " pdb=" C LYS L 376 " ideal model delta sigma weight residual 109.46 80.11 29.35 1.66e+00 3.63e-01 3.13e+02 angle pdb=" N ILE K 114 " pdb=" CA ILE K 114 " pdb=" C ILE K 114 " ideal model delta sigma weight residual 110.74 125.41 -14.67 9.10e-01 1.21e+00 2.60e+02 angle pdb=" C LYS L 376 " pdb=" CA LYS L 376 " pdb=" CB LYS L 376 " ideal model delta sigma weight residual 109.80 131.76 -21.96 1.64e+00 3.72e-01 1.79e+02 angle pdb=" C LEU N 20 " pdb=" CA LEU N 20 " pdb=" CB LEU N 20 " ideal model delta sigma weight residual 111.41 89.49 21.92 1.70e+00 3.46e-01 1.66e+02 angle pdb=" N ARG E 42 " pdb=" CA ARG E 42 " pdb=" C ARG E 42 " ideal model delta sigma weight residual 109.83 126.19 -16.36 1.27e+00 6.20e-01 1.66e+02 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 12345 35.32 - 70.63: 1663 70.63 - 105.95: 48 105.95 - 141.26: 0 141.26 - 176.58: 2 Dihedral angle restraints: 14058 sinusoidal: 7634 harmonic: 6424 Sorted by residual: dihedral pdb=" C TYR E 41 " pdb=" N TYR E 41 " pdb=" CA TYR E 41 " pdb=" CB TYR E 41 " ideal model delta harmonic sigma weight residual -122.60 -87.29 -35.31 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" C GLU N 212 " pdb=" N GLU N 212 " pdb=" CA GLU N 212 " pdb=" CB GLU N 212 " ideal model delta harmonic sigma weight residual -122.60 -143.91 21.31 0 2.50e+00 1.60e-01 7.27e+01 dihedral pdb=" C ARG L 347 " pdb=" N ARG L 347 " pdb=" CA ARG L 347 " pdb=" CB ARG L 347 " ideal model delta harmonic sigma weight residual -122.60 -140.32 17.72 0 2.50e+00 1.60e-01 5.02e+01 ... (remaining 14055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 3734 0.152 - 0.303: 147 0.303 - 0.455: 10 0.455 - 0.607: 2 0.607 - 0.758: 2 Chirality restraints: 3895 Sorted by residual: chirality pdb=" CA GLU N 212 " pdb=" N GLU N 212 " pdb=" C GLU N 212 " pdb=" CB GLU N 212 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA ARG L 347 " pdb=" N ARG L 347 " pdb=" C ARG L 347 " pdb=" CB ARG L 347 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA TYR E 41 " pdb=" N TYR E 41 " pdb=" C TYR E 41 " pdb=" CB TYR E 41 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.22e+00 ... (remaining 3892 not shown) Planarity restraints: 3373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP O 113 " -0.107 5.00e-02 4.00e+02 1.58e-01 3.99e+01 pdb=" N PRO O 114 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO O 114 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO O 114 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 308 " -0.029 2.00e-02 2.50e+03 5.91e-02 3.49e+01 pdb=" C PRO L 308 " 0.102 2.00e-02 2.50e+03 pdb=" O PRO L 308 " -0.040 2.00e-02 2.50e+03 pdb=" N PHE L 309 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 113 " 0.030 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C VAL K 113 " -0.098 2.00e-02 2.50e+03 pdb=" O VAL K 113 " 0.035 2.00e-02 2.50e+03 pdb=" N ILE K 114 " 0.034 2.00e-02 2.50e+03 ... (remaining 3370 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 267 2.57 - 3.15: 16532 3.15 - 3.73: 40353 3.73 - 4.32: 54944 4.32 - 4.90: 83927 Nonbonded interactions: 196023 Sorted by model distance: nonbonded pdb=" O LEU N 20 " pdb=" CG LEU N 20 " model vdw 1.984 3.470 nonbonded pdb=" O LYS L 376 " pdb=" OD1 ASP L 377 " model vdw 2.028 3.040 nonbonded pdb=" SG CYS K 256 " pdb=" O LEU K 302 " model vdw 2.085 3.400 nonbonded pdb=" OE2 GLU M 940 " pdb=" O SER M 994 " model vdw 2.152 3.040 nonbonded pdb=" NH1 ARG E 42 " pdb=" OP2 DC I 144 " model vdw 2.169 3.120 ... (remaining 196018 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 39 through 134) selection = (chain 'E' and (resid 39 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 121) selection = (chain 'H' and resid 30 through 121) } ncs_group { reference = (chain 'O' and (resid 85 through 106 or resid 113 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 126)) selection = (chain 'P' and resid 85 through 126) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.011 0.337 24661 Z= 0.694 Angle : 1.346 29.351 34584 Z= 0.905 Chirality : 0.074 0.758 3895 Planarity : 0.009 0.158 3373 Dihedral : 24.253 176.575 9906 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.55 % Favored : 93.36 % Rotamer: Outliers : 1.24 % Allowed : 10.17 % Favored : 88.59 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.54 (0.13), residues: 2153 helix: -4.68 (0.08), residues: 695 sheet: -2.69 (0.26), residues: 303 loop : -3.34 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.028 0.003 TYR L 272 PHE 0.033 0.003 PHE N 109 TRP 0.016 0.003 TRP L 105 HIS 0.008 0.002 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01038 / 0.69 (24660) covalent geometry : angle 1.34640 / 0.90 (34584) hydrogen bonds : bond 0.31239 / 20.41 ( 816) hydrogen bonds : angle 11.24194 / 7.71 ( 2030) metal coordination : bond 0.33729 / 22.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7913 (tt0) cc_final: 0.7441 (tt0) REVERT: A 90 MET cc_start: 0.7666 (mtt) cc_final: 0.7446 (mtp) REVERT: B 25 ASN cc_start: 0.8242 (m-40) cc_final: 0.7749 (m110) REVERT: E 81 ASP cc_start: 0.7555 (t70) cc_final: 0.6995 (t0) REVERT: F 53 GLU cc_start: 0.8319 (tp30) cc_final: 0.7683 (tp30) REVERT: F 77 LYS cc_start: 0.8937 (mttt) cc_final: 0.8382 (mmmt) REVERT: G 61 GLU cc_start: 0.7714 (tp30) cc_final: 0.7276 (tt0) REVERT: G 84 GLN cc_start: 0.8528 (tt0) cc_final: 0.8231 (tt0) REVERT: K 51 MET cc_start: 0.8082 (mpp) cc_final: 0.6730 (tmm) REVERT: K 54 TYR cc_start: 0.6428 (t80) cc_final: 0.6004 (t80) REVERT: K 279 MET cc_start: 0.4922 (mpp) cc_final: 0.4621 (mpp) REVERT: M 949 LYS cc_start: 0.7630 (ptpt) cc_final: 0.7333 (mptt) REVERT: N 22 HIS cc_start: 0.7723 (m90) cc_final: 0.7450 (m170) REVERT: N 64 MET cc_start: 0.6675 (ttt) cc_final: 0.5690 (tmm) REVERT: N 344 TRP cc_start: 0.6827 (m-10) cc_final: 0.6374 (m-10) REVERT: L 185 ARG cc_start: 0.6403 (ttm170) cc_final: 0.5263 (tpp80) REVERT: L 257 LEU cc_start: 0.5785 (pt) cc_final: 0.5559 (pt) REVERT: L 318 TYR cc_start: 0.3873 (t80) cc_final: 0.2426 (t80) REVERT: P 96 THR cc_start: 0.2673 (OUTLIER) cc_final: 0.2436 (m) outliers start: 24 outliers final: 9 residues processed: 259 average time/residue: 0.1576 time to fit residues: 63.4216 Evaluate side-chains 186 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain X residue 215 GLU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 84 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS H 81 ASN K 18 GLN K 97 HIS M 852 GLN M 936 ASN M 937 HIS N 77 GLN N 110 GLN N 161 GLN ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN N 276 GLN N 300 HIS N 431 GLN X 225 ASN X 296 ASN X 307 ASN ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 HIS L 295 ASN L 384 ASN O 98 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.156891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110589 restraints weight = 53210.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109703 restraints weight = 60115.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102389 restraints weight = 40255.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102582 restraints weight = 46162.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103011 restraints weight = 42906.374| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.094 24661 Z= 0.456 Angle : 0.993 12.376 34584 Z= 0.522 Chirality : 0.060 0.328 3895 Planarity : 0.007 0.075 3373 Dihedral : 28.218 173.410 5610 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 2.96 % Allowed : 16.44 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.65 (0.14), residues: 2153 helix: -3.48 (0.13), residues: 705 sheet: -2.52 (0.28), residues: 288 loop : -3.02 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 900 TYR 0.030 0.003 TYR G 50 PHE 0.032 0.003 PHE D 67 TRP 0.016 0.002 TRP N 305 HIS 0.009 0.002 HIS K 97 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.46 (24660) covalent geometry : angle 0.99274 / 0.52 (34584) hydrogen bonds : bond 0.09382 / 6.10 ( 816) hydrogen bonds : angle 6.33137 / 4.41 ( 2030) metal coordination : bond 0.01073 / 0.72 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9284 (mt) cc_final: 0.9036 (mp) REVERT: B 25 ASN cc_start: 0.8152 (m-40) cc_final: 0.7719 (m110) REVERT: C 73 ASN cc_start: 0.8193 (m-40) cc_final: 0.7922 (t0) REVERT: D 110 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: E 81 ASP cc_start: 0.7640 (t70) cc_final: 0.7154 (t0) REVERT: F 53 GLU cc_start: 0.8167 (tp30) cc_final: 0.7552 (tp30) REVERT: G 61 GLU cc_start: 0.7635 (tp30) cc_final: 0.7380 (tt0) REVERT: K 51 MET cc_start: 0.7959 (mpp) cc_final: 0.6753 (tmm) REVERT: K 68 HIS cc_start: 0.6013 (m-70) cc_final: 0.5797 (m-70) REVERT: K 97 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.6052 (t-170) REVERT: K 279 MET cc_start: 0.5025 (mpp) cc_final: 0.3595 (mpp) REVERT: N 4 LEU cc_start: 0.6741 (mt) cc_final: 0.6478 (mp) REVERT: L 318 TYR cc_start: 0.3796 (t80) cc_final: 0.2353 (t80) REVERT: P 81 MET cc_start: 0.3753 (tpp) cc_final: 0.3462 (ptp) outliers start: 57 outliers final: 38 residues processed: 225 average time/residue: 0.1443 time to fit residues: 52.8282 Evaluate side-chains 201 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 74 CYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 766 ILE Chi-restraints excluded: chain M residue 854 THR Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 223 ILE Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain L residue 293 PHE Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 170 optimal weight: 0.9990 chunk 196 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 84 GLN F 25 ASN F 75 HIS F 93 GLN K 18 GLN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.161382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116099 restraints weight = 53383.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116487 restraints weight = 56057.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116038 restraints weight = 45024.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115663 restraints weight = 33948.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115858 restraints weight = 33872.964| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24661 Z= 0.151 Angle : 0.690 10.824 34584 Z= 0.387 Chirality : 0.049 0.357 3895 Planarity : 0.005 0.056 3373 Dihedral : 27.783 174.799 5600 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 1.92 % Allowed : 18.57 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.81 (0.16), residues: 2153 helix: -2.41 (0.17), residues: 702 sheet: -2.34 (0.27), residues: 319 loop : -2.67 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.029 0.002 TYR L 40 PHE 0.018 0.001 PHE K 211 TRP 0.019 0.001 TRP N 95 HIS 0.007 0.001 HIS K 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (24660) covalent geometry : angle 0.68976 / 0.39 (34584) hydrogen bonds : bond 0.06966 / 4.58 ( 816) hydrogen bonds : angle 5.40664 / 3.78 ( 2030) metal coordination : bond 0.00378 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.807 Fit side-chains REVERT: B 25 ASN cc_start: 0.8173 (m-40) cc_final: 0.7624 (m110) REVERT: C 73 ASN cc_start: 0.8178 (m-40) cc_final: 0.7890 (t0) REVERT: D 68 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7330 (mt-10) REVERT: D 110 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 81 ASP cc_start: 0.7281 (t70) cc_final: 0.6829 (t0) REVERT: E 94 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7251 (mt-10) REVERT: E 125 GLN cc_start: 0.8056 (mt0) cc_final: 0.7838 (mt0) REVERT: H 88 SER cc_start: 0.9205 (t) cc_final: 0.8965 (t) REVERT: K 51 MET cc_start: 0.7270 (mpp) cc_final: 0.6230 (tmm) REVERT: K 279 MET cc_start: 0.4982 (mpp) cc_final: 0.3561 (mpp) REVERT: N 151 PHE cc_start: 0.4923 (OUTLIER) cc_final: 0.4707 (m-10) REVERT: L 293 PHE cc_start: 0.6321 (OUTLIER) cc_final: 0.6120 (m-10) REVERT: L 318 TYR cc_start: 0.3112 (t80) cc_final: 0.2186 (t80) REVERT: L 375 PRO cc_start: 0.1974 (Cg_endo) cc_final: 0.1523 (Cg_exo) outliers start: 37 outliers final: 18 residues processed: 227 average time/residue: 0.1462 time to fit residues: 53.5708 Evaluate side-chains 196 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain M residue 854 THR Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 223 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 279 MET Chi-restraints excluded: chain L residue 293 PHE Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 160 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.0570 chunk 194 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 81 ASN E 68 GLN G 84 GLN K 18 GLN ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.162153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118814 restraints weight = 53310.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116043 restraints weight = 57058.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112102 restraints weight = 44925.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112176 restraints weight = 39979.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112463 restraints weight = 39871.068| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24661 Z= 0.138 Angle : 0.644 7.805 34584 Z= 0.361 Chirality : 0.048 0.366 3895 Planarity : 0.004 0.050 3373 Dihedral : 27.568 178.170 5598 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.96 % Allowed : 18.67 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.29 (0.16), residues: 2153 helix: -1.77 (0.18), residues: 700 sheet: -2.17 (0.27), residues: 311 loop : -2.48 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 39 TYR 0.015 0.001 TYR C 57 PHE 0.015 0.001 PHE N 419 TRP 0.008 0.001 TRP K 282 HIS 0.006 0.001 HIS M 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (24660) covalent geometry : angle 0.64426 / 0.36 (34584) hydrogen bonds : bond 0.06082 / 4.06 ( 816) hydrogen bonds : angle 4.92307 / 3.44 ( 2030) metal coordination : bond 0.00092 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8243 (m-40) cc_final: 0.7738 (m110) REVERT: D 68 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7775 (mt-10) REVERT: E 81 ASP cc_start: 0.7267 (t70) cc_final: 0.6815 (t0) REVERT: E 125 GLN cc_start: 0.8039 (mt0) cc_final: 0.7830 (mt0) REVERT: H 88 SER cc_start: 0.9178 (t) cc_final: 0.8922 (t) REVERT: K 279 MET cc_start: 0.4959 (mpp) cc_final: 0.3548 (mpp) REVERT: M 893 ARG cc_start: 0.7188 (ptt-90) cc_final: 0.6968 (mtm110) REVERT: M 904 TYR cc_start: 0.7877 (m-10) cc_final: 0.7144 (m-80) REVERT: N 4 LEU cc_start: 0.6561 (mt) cc_final: 0.6311 (mp) REVERT: N 333 MET cc_start: 0.8445 (mmm) cc_final: 0.8215 (tpt) REVERT: L 87 LYS cc_start: 0.1613 (ttmt) cc_final: 0.0219 (tppp) REVERT: L 375 PRO cc_start: 0.1769 (Cg_endo) cc_final: 0.1342 (Cg_exo) REVERT: P 81 MET cc_start: 0.4328 (tpp) cc_final: 0.3988 (ptp) REVERT: P 96 THR cc_start: 0.2000 (OUTLIER) cc_final: 0.1795 (p) outliers start: 57 outliers final: 30 residues processed: 238 average time/residue: 0.1445 time to fit residues: 55.3125 Evaluate side-chains 206 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 886 GLU Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 279 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain P residue 82 ILE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 1 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 73 ASN E 68 GLN N 161 GLN ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.162040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117278 restraints weight = 52949.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116155 restraints weight = 56799.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111015 restraints weight = 42445.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110992 restraints weight = 40407.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111290 restraints weight = 39732.400| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24661 Z= 0.142 Angle : 0.626 6.825 34584 Z= 0.352 Chirality : 0.047 0.305 3895 Planarity : 0.004 0.048 3373 Dihedral : 27.418 179.789 5598 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.96 % Allowed : 19.55 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.17), residues: 2153 helix: -1.43 (0.19), residues: 706 sheet: -1.96 (0.28), residues: 309 loop : -2.37 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 339 TYR 0.017 0.001 TYR L 318 PHE 0.019 0.001 PHE L 293 TRP 0.008 0.001 TRP K 282 HIS 0.004 0.001 HIS M 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (24660) covalent geometry : angle 0.62635 / 0.35 (34584) hydrogen bonds : bond 0.05814 / 3.86 ( 816) hydrogen bonds : angle 4.76011 / 3.32 ( 2030) metal coordination : bond 0.00103 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.711 Fit side-chains REVERT: D 68 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7755 (mt-10) REVERT: E 81 ASP cc_start: 0.7269 (t70) cc_final: 0.6831 (t0) REVERT: G 84 GLN cc_start: 0.8774 (tt0) cc_final: 0.8514 (tt0) REVERT: H 88 SER cc_start: 0.9182 (t) cc_final: 0.8946 (t) REVERT: K 51 MET cc_start: 0.7750 (mpp) cc_final: 0.7395 (mpp) REVERT: K 97 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6017 (t-170) REVERT: K 279 MET cc_start: 0.4884 (mpp) cc_final: 0.3485 (mpp) REVERT: M 893 ARG cc_start: 0.7127 (ptt-90) cc_final: 0.6633 (ptt90) REVERT: M 904 TYR cc_start: 0.7806 (m-10) cc_final: 0.7128 (m-80) REVERT: L 237 ARG cc_start: 0.4099 (mtp180) cc_final: 0.2976 (tpm170) outliers start: 57 outliers final: 39 residues processed: 231 average time/residue: 0.1424 time to fit residues: 53.3339 Evaluate side-chains 211 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 886 GLU Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 291 VAL Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 279 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 396 VAL Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 196 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 160 optimal weight: 0.0070 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 113 HIS ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 HIS O 92 ASN ** P 92 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 = 0.4360 r_free = 0.4360 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118006 restraints weight = 53255.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116896 restraints weight = 52843.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111516 restraints weight = 34188.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111422 restraints weight = 35908.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111743 restraints weight = 37405.908| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24661 Z= 0.128 Angle : 0.607 8.912 34584 Z= 0.342 Chirality : 0.046 0.310 3895 Planarity : 0.004 0.043 3373 Dihedral : 27.311 179.832 5598 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 2.90 % Allowed : 20.85 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.74 (0.17), residues: 2153 helix: -1.16 (0.19), residues: 707 sheet: -1.79 (0.28), residues: 307 loop : -2.28 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.017 0.001 TYR M 959 PHE 0.033 0.001 PHE L 293 TRP 0.010 0.001 TRP N 100 HIS 0.002 0.000 HIS K 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (24660) covalent geometry : angle 0.60737 / 0.34 (34584) hydrogen bonds : bond 0.05601 / 3.72 ( 816) hydrogen bonds : angle 4.59995 / 3.21 ( 2030) metal coordination : bond 0.00086 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.622 Fit side-chains REVERT: D 68 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 81 ASP cc_start: 0.7276 (t70) cc_final: 0.6851 (t0) REVERT: K 51 MET cc_start: 0.7786 (mpp) cc_final: 0.7454 (mpp) REVERT: K 97 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6071 (t-170) REVERT: K 197 TRP cc_start: 0.4555 (m100) cc_final: 0.3960 (m100) REVERT: K 279 MET cc_start: 0.4826 (mpp) cc_final: 0.3453 (mpp) REVERT: M 893 ARG cc_start: 0.7167 (ptt-90) cc_final: 0.6730 (ptt90) REVERT: M 904 TYR cc_start: 0.7794 (m-10) cc_final: 0.7079 (m-80) REVERT: N 333 MET cc_start: 0.8611 (mmm) cc_final: 0.8236 (tpt) REVERT: L 185 ARG cc_start: 0.6485 (mtt180) cc_final: 0.5426 (mmm-85) REVERT: L 237 ARG cc_start: 0.4073 (mtp180) cc_final: 0.2933 (tpm170) outliers start: 56 outliers final: 37 residues processed: 231 average time/residue: 0.1443 time to fit residues: 53.7402 Evaluate side-chains 210 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 886 GLU Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 291 VAL Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 428 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 377 ASP Chi-restraints excluded: chain P residue 82 ILE Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 183 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 chunk 9 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 204 optimal weight: 0.2980 chunk 177 optimal weight: 5.9990 chunk 135 optimal weight: 0.0970 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** 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 = 0.4368 r_free = 0.4368 target = 0.163341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117557 restraints weight = 53020.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118295 restraints weight = 50655.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115000 restraints weight = 34924.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114434 restraints weight = 36408.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114623 restraints weight = 37325.937| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24661 Z= 0.121 Angle : 0.593 8.346 34584 Z= 0.333 Chirality : 0.045 0.417 3895 Planarity : 0.004 0.041 3373 Dihedral : 27.202 179.998 5597 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 2.28 % Allowed : 21.58 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.47 (0.17), residues: 2153 helix: -0.78 (0.20), residues: 699 sheet: -1.79 (0.28), residues: 312 loop : -2.17 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.016 0.001 TYR L 39 PHE 0.023 0.001 PHE L 293 TRP 0.012 0.001 TRP K 282 HIS 0.002 0.000 HIS L 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (24660) covalent geometry : angle 0.59307 / 0.33 (34584) hydrogen bonds : bond 0.05375 / 3.57 ( 816) hydrogen bonds : angle 4.45403 / 3.11 ( 2030) metal coordination : bond 0.00089 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.583 Fit side-chains REVERT: D 68 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 81 ASP cc_start: 0.7294 (t70) cc_final: 0.6901 (t0) REVERT: E 131 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8374 (ttp-110) REVERT: K 51 MET cc_start: 0.7559 (mpp) cc_final: 0.7269 (mpp) REVERT: K 97 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.5717 (t-170) REVERT: K 193 TYR cc_start: 0.7036 (m-80) cc_final: 0.6462 (m-80) REVERT: K 197 TRP cc_start: 0.4520 (m100) cc_final: 0.3939 (m100) REVERT: K 279 MET cc_start: 0.4837 (mpp) cc_final: 0.3478 (mpp) REVERT: M 893 ARG cc_start: 0.7239 (ptt-90) cc_final: 0.6791 (ptt90) REVERT: M 904 TYR cc_start: 0.7667 (m-10) cc_final: 0.7047 (m-80) REVERT: N 333 MET cc_start: 0.8468 (mmm) cc_final: 0.8180 (tpt) REVERT: L 16 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3350 (mp) REVERT: L 185 ARG cc_start: 0.6354 (mtt180) cc_final: 0.5327 (mmm-85) REVERT: L 237 ARG cc_start: 0.3990 (mtp180) cc_final: 0.2835 (tpm170) outliers start: 44 outliers final: 34 residues processed: 227 average time/residue: 0.1423 time to fit residues: 52.1922 Evaluate side-chains 214 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 291 VAL Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 10 optimal weight: 0.0040 chunk 55 optimal weight: 1.9990 chunk 184 optimal weight: 0.0170 chunk 168 optimal weight: 0.0470 chunk 112 optimal weight: 0.2980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 166 HIS ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.163919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.118214 restraints weight = 53194.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118433 restraints weight = 53481.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117579 restraints weight = 41222.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116816 restraints weight = 33230.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117113 restraints weight = 33303.465| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24661 Z= 0.117 Angle : 0.584 7.765 34584 Z= 0.329 Chirality : 0.045 0.361 3895 Planarity : 0.004 0.040 3373 Dihedral : 27.104 179.979 5597 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.49 % Allowed : 21.47 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.17), residues: 2153 helix: -0.52 (0.20), residues: 702 sheet: -1.64 (0.28), residues: 310 loop : -2.15 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.010 0.001 TYR L 40 PHE 0.016 0.001 PHE L 293 TRP 0.024 0.001 TRP N 95 HIS 0.003 0.000 HIS L 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (24660) covalent geometry : angle 0.58362 / 0.33 (34584) hydrogen bonds : bond 0.05268 / 3.50 ( 816) hydrogen bonds : angle 4.32248 / 3.02 ( 2030) metal coordination : bond 0.00066 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7563 (mt-10) REVERT: E 81 ASP cc_start: 0.7173 (t70) cc_final: 0.6806 (t0) REVERT: H 30 ARG cc_start: 0.7177 (mmm160) cc_final: 0.6805 (mtt-85) REVERT: K 97 HIS cc_start: 0.6155 (OUTLIER) cc_final: 0.5575 (t-170) REVERT: K 193 TYR cc_start: 0.7088 (m-80) cc_final: 0.6662 (m-80) REVERT: K 197 TRP cc_start: 0.4459 (m100) cc_final: 0.3889 (m100) REVERT: K 279 MET cc_start: 0.4791 (mpp) cc_final: 0.3478 (mpp) REVERT: M 758 PHE cc_start: 0.5221 (m-80) cc_final: 0.4968 (m-80) REVERT: M 904 TYR cc_start: 0.7547 (m-10) cc_final: 0.6989 (m-80) REVERT: N 3 ASN cc_start: 0.6954 (m110) cc_final: 0.6752 (t0) REVERT: N 64 MET cc_start: 0.6876 (tmm) cc_final: 0.6668 (tmt) REVERT: N 333 MET cc_start: 0.8400 (mmm) cc_final: 0.8077 (tpt) REVERT: L 87 LYS cc_start: 0.2134 (ttmt) cc_final: 0.0541 (tppp) REVERT: L 237 ARG cc_start: 0.3958 (mtp180) cc_final: 0.2915 (tpm170) REVERT: L 306 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6268 (tt) outliers start: 48 outliers final: 37 residues processed: 227 average time/residue: 0.1478 time to fit residues: 54.6326 Evaluate side-chains 221 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 886 GLU Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 957 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 166 HIS Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 187 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 134 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 201 optimal weight: 30.0000 chunk 189 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 GLN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.163597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119606 restraints weight = 53425.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119143 restraints weight = 57371.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114944 restraints weight = 38014.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.114628 restraints weight = 35246.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114825 restraints weight = 37619.838| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24661 Z= 0.126 Angle : 0.587 7.804 34584 Z= 0.329 Chirality : 0.045 0.311 3895 Planarity : 0.004 0.040 3373 Dihedral : 27.077 179.954 5596 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 2.33 % Allowed : 21.68 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.17), residues: 2153 helix: -0.43 (0.20), residues: 702 sheet: -1.59 (0.28), residues: 312 loop : -2.11 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.014 0.001 TYR N 346 PHE 0.013 0.001 PHE L 293 TRP 0.012 0.001 TRP N 95 HIS 0.039 0.001 HIS N 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (24660) covalent geometry : angle 0.58684 / 0.33 (34584) hydrogen bonds : bond 0.05270 / 3.51 ( 816) hydrogen bonds : angle 4.28990 / 3.00 ( 2030) metal coordination : bond 0.00076 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7570 (mt-10) REVERT: E 81 ASP cc_start: 0.7229 (t70) cc_final: 0.6825 (t0) REVERT: H 30 ARG cc_start: 0.7180 (mmm160) cc_final: 0.6759 (mtt-85) REVERT: K 97 HIS cc_start: 0.6406 (OUTLIER) cc_final: 0.5829 (t-170) REVERT: K 107 MET cc_start: 0.6622 (ptm) cc_final: 0.6352 (ptm) REVERT: K 193 TYR cc_start: 0.7080 (m-80) cc_final: 0.6717 (m-80) REVERT: K 197 TRP cc_start: 0.4350 (m100) cc_final: 0.3776 (m100) REVERT: K 279 MET cc_start: 0.4764 (mpp) cc_final: 0.3443 (mpp) REVERT: M 758 PHE cc_start: 0.5253 (m-80) cc_final: 0.4965 (m-80) REVERT: M 904 TYR cc_start: 0.7684 (m-10) cc_final: 0.7088 (m-80) REVERT: N 333 MET cc_start: 0.8455 (mmm) cc_final: 0.8001 (tpt) REVERT: L 16 LEU cc_start: 0.3753 (OUTLIER) cc_final: 0.3460 (mp) REVERT: L 87 LYS cc_start: 0.1856 (ttmt) cc_final: 0.0115 (tppt) REVERT: L 237 ARG cc_start: 0.4003 (mtp180) cc_final: 0.2955 (tpm170) REVERT: L 306 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6128 (tt) outliers start: 45 outliers final: 38 residues processed: 219 average time/residue: 0.1358 time to fit residues: 48.7515 Evaluate side-chains 224 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 957 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 76 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.115643 restraints weight = 52829.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113331 restraints weight = 51649.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110236 restraints weight = 37096.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109125 restraints weight = 42661.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109327 restraints weight = 42703.361| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24661 Z= 0.200 Angle : 0.648 8.380 34584 Z= 0.353 Chirality : 0.047 0.307 3895 Planarity : 0.004 0.044 3373 Dihedral : 27.204 179.117 5596 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 2.33 % Allowed : 21.94 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.17), residues: 2153 helix: -0.67 (0.19), residues: 699 sheet: -1.68 (0.28), residues: 324 loop : -2.06 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.015 0.001 TYR G 50 PHE 0.015 0.001 PHE N 35 TRP 0.022 0.001 TRP N 190 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (24660) covalent geometry : angle 0.64812 / 0.35 (34584) hydrogen bonds : bond 0.05824 / 3.89 ( 816) hydrogen bonds : angle 4.45562 / 3.10 ( 2030) metal coordination : bond 0.00140 / 0.09 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4306 Ramachandran restraints generated. 2153 Oldfield, 0 Emsley, 2153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 ASP cc_start: 0.8460 (t0) cc_final: 0.8212 (t0) REVERT: D 68 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7652 (mt-10) REVERT: E 81 ASP cc_start: 0.7410 (t70) cc_final: 0.6980 (t0) REVERT: F 53 GLU cc_start: 0.7539 (tp30) cc_final: 0.7141 (tp30) REVERT: K 97 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6181 (t-170) REVERT: K 107 MET cc_start: 0.6796 (ptm) cc_final: 0.6551 (ptm) REVERT: K 193 TYR cc_start: 0.7103 (m-80) cc_final: 0.6861 (m-80) REVERT: K 197 TRP cc_start: 0.4480 (m100) cc_final: 0.3877 (m100) REVERT: M 904 TYR cc_start: 0.7849 (m-10) cc_final: 0.7171 (m-80) REVERT: N 333 MET cc_start: 0.8478 (mmm) cc_final: 0.7982 (tpt) REVERT: L 87 LYS cc_start: 0.1685 (ttmt) cc_final: 0.0033 (tppt) REVERT: L 237 ARG cc_start: 0.4007 (mtp180) cc_final: 0.2898 (tpm170) REVERT: L 306 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6106 (tt) outliers start: 45 outliers final: 39 residues processed: 209 average time/residue: 0.1404 time to fit residues: 48.4312 Evaluate side-chains 210 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 886 GLU Chi-restraints excluded: chain M residue 896 VAL Chi-restraints excluded: chain M residue 957 VAL Chi-restraints excluded: chain M residue 966 THR Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 335 ILE Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain X residue 221 SER Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 162 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 chunk 238 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN G 84 GLN ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 ASN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.160201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115486 restraints weight = 52890.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110133 restraints weight = 57517.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106731 restraints weight = 46256.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106084 restraints weight = 45786.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106732 restraints weight = 41547.094| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24661 Z= 0.245 Angle : 0.688 8.857 34584 Z= 0.371 Chirality : 0.048 0.306 3895 Planarity : 0.004 0.049 3373 Dihedral : 27.302 179.102 5596 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 2.54 % Allowed : 21.89 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.50 (0.17), residues: 2153 helix: -1.01 (0.19), residues: 706 sheet: -1.67 (0.28), residues: 318 loop : -2.10 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 116 TYR 0.018 0.002 TYR G 50 PHE 0.016 0.002 PHE D 67 TRP 0.017 0.002 TRP N 100 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (24660) covalent geometry : angle 0.68810 / 0.37 (34584) hydrogen bonds : bond 0.06033 / 4.03 ( 816) hydrogen bonds : angle 4.60287 / 3.20 ( 2030) metal coordination : bond 0.00200 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3958.11 seconds wall clock time: 68 minutes 58.01 seconds (4138.01 seconds total)