Starting phenix.real_space_refine on Fri Jun 13 11:46:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy4_11549/06_2025/6zy4_11549.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9597 2.51 5 N 2504 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14902 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1013 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 793 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 999 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 999 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 794 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 941 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 724 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 734 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1982 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1972 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1949 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.10, per 1000 atoms: 0.68 Number of scatterers: 14902 At special positions: 0 Unit cell: (99.372, 126.75, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 4 15.00 Mg 2 11.99 O 2726 8.00 N 2504 7.00 C 9597 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: 3.92 Conformation dependent library (CDL) restraints added in 2.1 seconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 24 sheets defined 35.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.572A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.621A pdb=" N LEU A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 removed outlier: 3.653A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 removed outlier: 3.737A pdb=" N ILE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 24 removed outlier: 3.865A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.622A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 23 removed outlier: 3.662A pdb=" N ILE J 8 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.545A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN K 149 " --> pdb=" O ASP K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 24 removed outlier: 4.029A pdb=" N ILE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE L 13 " --> pdb=" O TRP L 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 removed outlier: 3.689A pdb=" N LEU L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.786A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.016A pdb=" N GLU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.934A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.926A pdb=" N THR F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.636A pdb=" N VAL F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 4.125A pdb=" N GLU F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 removed outlier: 3.506A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 130 removed outlier: 3.853A pdb=" N GLU F 130 " --> pdb=" O MET F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 130' Processing helix chain 'F' and resid 148 through 157 removed outlier: 3.685A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 4.348A pdb=" N GLY F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.717A pdb=" N VAL F 208 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'G' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.985A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR G 82 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 removed outlier: 3.750A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 107 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 126 removed outlier: 3.507A pdb=" N HIS G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 133 removed outlier: 3.963A pdb=" N VAL G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 157 removed outlier: 3.762A pdb=" N ARG G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 181 removed outlier: 3.523A pdb=" N GLY G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 192 removed outlier: 3.730A pdb=" N LEU G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 removed outlier: 3.672A pdb=" N LEU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP G 245 " --> pdb=" O ARG G 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 245' Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.554A pdb=" N HIS E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 29 removed outlier: 3.552A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 58 through 74 removed outlier: 3.581A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 72 " --> pdb=" O MET E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.602A pdb=" N LEU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.877A pdb=" N LEU E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.565A pdb=" N VAL E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.540A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 136 removed outlier: 4.032A pdb=" N MET E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 175 removed outlier: 3.673A pdb=" N LEU E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Proline residue: E 156 - end of helix removed outlier: 3.668A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.971A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 200 through 205 removed outlier: 3.697A pdb=" N LYS E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 223 removed outlier: 3.778A pdb=" N THR E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 247 removed outlier: 3.675A pdb=" N THR E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 11 through 29 removed outlier: 3.540A pdb=" N LYS H 15 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.934A pdb=" N GLY H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 86 Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 99 through 112 removed outlier: 3.707A pdb=" N VAL H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA H 105 " --> pdb=" O PRO H 101 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 128 through 134 removed outlier: 3.675A pdb=" N MET H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 134' Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.953A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 175 removed outlier: 3.742A pdb=" N ALA H 164 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 175 " --> pdb=" O SER H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 189 removed outlier: 4.047A pdb=" N MET H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 206 removed outlier: 3.573A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 removed outlier: 3.820A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE H 219 " --> pdb=" O TRP H 215 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 247 removed outlier: 4.389A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER H 242 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 245 " --> pdb=" O HIS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 removed outlier: 7.268A pdb=" N THR A 83 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 71 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG A 81 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ILE A 134 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR A 43 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.014A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 60 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 66 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 59 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 99 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 60 removed outlier: 6.853A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY D 66 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 87 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D 70 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 83 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 72 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ILE D 134 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR D 43 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 110 through 115 removed outlier: 3.520A pdb=" N ALA D 113 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 100 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU D 99 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 40 through 41 removed outlier: 3.903A pdb=" N TYR I 40 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 86 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 40 through 41 removed outlier: 3.903A pdb=" N TYR I 40 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 86 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR I 43 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.080A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 110 through 115 removed outlier: 6.320A pdb=" N LEU I 99 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 39 through 41 removed outlier: 3.615A pdb=" N THR J 83 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU J 87 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY J 66 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 43 through 44 removed outlier: 7.033A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 40 through 41 removed outlier: 3.778A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 71 through 73 removed outlier: 7.357A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 64 through 66 removed outlier: 6.769A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 100 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.601A pdb=" N LEU L 84 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ILE L 134 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 64 through 67 removed outlier: 3.865A pdb=" N GLY L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB8, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AB9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.579A pdb=" N GLU F 64 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 165 through 168 removed outlier: 3.541A pdb=" N ILE F 166 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS F 214 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 218 through 219 removed outlier: 3.511A pdb=" N ALA F 219 " --> pdb=" O LYS F 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 7 through 11 removed outlier: 4.953A pdb=" N VAL G 9 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL G 31 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET G 11 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 29 " --> pdb=" O MET G 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 165 through 168 removed outlier: 3.621A pdb=" N HIS G 214 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 218 through 219 361 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4759 1.34 - 1.46: 2897 1.46 - 1.58: 7373 1.58 - 1.69: 6 1.69 - 1.81: 126 Bond restraints: 15161 Sorted by residual: bond pdb=" C TYR F 108 " pdb=" N PRO F 109 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C GLU K 37 " pdb=" N PRO K 38 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" CA THR J 39 " pdb=" C THR J 39 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.08e-02 8.57e+03 2.71e+00 bond pdb=" CA GLY B 11 " pdb=" C GLY B 11 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.34e+00 bond pdb=" N PHE G 172 " pdb=" CA PHE G 172 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.05e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 20385 3.12 - 6.24: 204 6.24 - 9.36: 29 9.36 - 12.48: 9 12.48 - 15.61: 2 Bond angle restraints: 20629 Sorted by residual: angle pdb=" CA LEU F 265 " pdb=" CB LEU F 265 " pdb=" CG LEU F 265 " ideal model delta sigma weight residual 116.30 131.91 -15.61 3.50e+00 8.16e-02 1.99e+01 angle pdb=" N VAL F 205 " pdb=" CA VAL F 205 " pdb=" C VAL F 205 " ideal model delta sigma weight residual 108.88 118.36 -9.48 2.16e+00 2.14e-01 1.93e+01 angle pdb=" CA LEU G 265 " pdb=" CB LEU G 265 " pdb=" CG LEU G 265 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ASP G 220 " pdb=" N LYS G 221 " pdb=" CA LYS G 221 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ALA F 107 " pdb=" N TYR F 108 " pdb=" CA TYR F 108 " ideal model delta sigma weight residual 120.58 125.62 -5.04 1.32e+00 5.74e-01 1.46e+01 ... (remaining 20624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 8788 31.94 - 63.88: 205 63.88 - 95.83: 8 95.83 - 127.77: 2 127.77 - 159.71: 4 Dihedral angle restraints: 9007 sinusoidal: 3385 harmonic: 5622 Sorted by residual: dihedral pdb=" C5' ADP G 301 " pdb=" O5' ADP G 301 " pdb=" PA ADP G 301 " pdb=" O2A ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.71 -159.71 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP F 301 " pdb=" O5' ADP F 301 " pdb=" PA ADP F 301 " pdb=" O2A ADP F 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.68 -159.68 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP G 301 " pdb=" O3A ADP G 301 " pdb=" PA ADP G 301 " pdb=" PB ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 74.69 -134.69 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 9004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1945 0.051 - 0.101: 434 0.101 - 0.152: 115 0.152 - 0.202: 25 0.202 - 0.253: 2 Chirality restraints: 2521 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE G 65 " pdb=" CA ILE G 65 " pdb=" CG1 ILE G 65 " pdb=" CG2 ILE G 65 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2518 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 145 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO E 146 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 205 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO G 206 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 206 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 206 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 145 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO H 146 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.030 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4650 2.83 - 3.35: 11934 3.35 - 3.87: 23578 3.87 - 4.38: 25608 4.38 - 4.90: 43735 Nonbonded interactions: 109505 Sorted by model distance: nonbonded pdb=" OG1 THR I 39 " pdb=" O ILE I 86 " model vdw 2.314 3.040 nonbonded pdb=" O ASN B 89 " pdb=" OH TYR G 261 " model vdw 2.322 3.040 nonbonded pdb=" O LEU H 90 " pdb=" OG SER H 94 " model vdw 2.323 3.040 nonbonded pdb=" O ILE H 58 " pdb=" OG SER H 62 " model vdw 2.331 3.040 nonbonded pdb=" O ILE E 58 " pdb=" OG SER E 62 " model vdw 2.333 3.040 ... (remaining 109500 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 3 through 25 or resid 40 through 69 or (resid 70 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or r \ esid 86 or (resid 87 through 88 and (name N or name CA or name C or name O or na \ me CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N \ or name CA or name C or name O or name CB )) or resid 96 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throug \ h 116 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB )) or resid 142 through 143 or (resid 144 through 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 152)) selection = (chain 'I' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 or (res \ id 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (r \ esid 76 and (name N or name CA or name C or name O or name CB )) or resid 77 thr \ ough 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or \ resid 86 through 87 or (resid 88 and (name N or name CA or name C or name O or \ name CB )) or resid 89 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 116 or (resid 130 throu \ gh 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 through 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 152)) selection = (chain 'J' and (resid 3 through 25 or resid 40 through 70 or (resid 71 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 86 or (resid 87 through 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 116 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 142 or (r \ esid 143 through 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 152)) selection = (chain 'L' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 70 or (resid \ 71 through 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 84 or (resid 85 and (name N or name CA or name C or name O or name C \ B )) or resid 86 or (resid 87 through 88 and (name N or name CA or name C or nam \ e O or name CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or \ name CA or name C or name O or name CB )) or resid 93 through 116 or (resid 130 \ and (name N or name CA or name C or name O or name CB )) or resid 131 through 14 \ 0 or (resid 141 and (name N or name CA or name C or name O or name CB )) or resi \ d 142 through 143 or (resid 144 through 145 and (name N or name CA or name C or \ name O or name CB )) or resid 146 through 152)) } ncs_group { reference = (chain 'B' and (resid 4 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98)) selection = (chain 'C' and (resid 4 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 98)) } ncs_group { reference = (chain 'D' and (resid 37 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 88 or (resid 89 and ( \ name N or name CA or name C or name O or name CB )) or resid 90 through 94 or (r \ esid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 117 or (resid 129 and (name N or name CA or name C or name \ O or name CB )) or resid 130 through 152)) selection = (chain 'K' and (resid 37 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 117 or resid 129 through 152)) } ncs_group { reference = chain 'E' selection = (chain 'H' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 259)) } ncs_group { reference = (chain 'F' and (resid 6 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 267 or \ resid 301 through 302)) selection = (chain 'G' and (resid 6 through 248 or (resid 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 267 or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 36.490 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.003 0.044 15161 Z= 0.155 Angle : 0.797 15.605 20629 Z= 0.393 Chirality : 0.049 0.253 2521 Planarity : 0.005 0.057 2568 Dihedral : 13.498 159.710 5397 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.13), residues: 1934 helix: -5.17 (0.04), residues: 649 sheet: -3.13 (0.27), residues: 233 loop : -3.32 (0.15), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 195 HIS 0.004 0.000 HIS F 113 PHE 0.008 0.001 PHE G 172 TYR 0.010 0.001 TYR I 40 ARG 0.003 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.34396 ( 361) hydrogen bonds : angle 10.92594 ( 1032) covalent geometry : bond 0.00292 (15161) covalent geometry : angle 0.79741 (20629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8991 (m-10) cc_final: 0.8748 (m-10) REVERT: A 46 PHE cc_start: 0.7031 (m-80) cc_final: 0.6755 (m-80) REVERT: A 95 ASP cc_start: 0.7357 (p0) cc_final: 0.6828 (p0) REVERT: A 138 LYS cc_start: 0.8110 (tttt) cc_final: 0.7643 (tptp) REVERT: A 141 MET cc_start: 0.7644 (mmt) cc_final: 0.7279 (tpt) REVERT: A 144 GLU cc_start: 0.7877 (pp20) cc_final: 0.7162 (mp0) REVERT: D 57 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8306 (Cg_exo) REVERT: D 95 ASP cc_start: 0.5560 (m-30) cc_final: 0.4095 (t0) REVERT: D 136 ASP cc_start: 0.8096 (t0) cc_final: 0.7822 (m-30) REVERT: I 7 GLU cc_start: 0.8919 (pt0) cc_final: 0.7668 (tm-30) REVERT: I 8 ILE cc_start: 0.9530 (mt) cc_final: 0.8699 (mt) REVERT: I 60 ILE cc_start: 0.9209 (mt) cc_final: 0.8784 (tt) REVERT: J 4 LYS cc_start: 0.7840 (tppt) cc_final: 0.7223 (tttt) REVERT: J 60 ILE cc_start: 0.9125 (pt) cc_final: 0.8685 (mm) REVERT: J 92 HIS cc_start: 0.8173 (m90) cc_final: 0.7878 (m-70) REVERT: J 102 ARG cc_start: 0.9164 (mtt180) cc_final: 0.8485 (ttp-110) REVERT: J 111 TYR cc_start: 0.8752 (p90) cc_final: 0.8507 (p90) REVERT: J 138 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6303 (tptp) REVERT: K 53 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8084 (mmtt) REVERT: K 145 ASP cc_start: 0.9274 (m-30) cc_final: 0.8940 (p0) REVERT: L 85 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7720 (mp0) REVERT: B 8 MET cc_start: 0.8986 (tpt) cc_final: 0.8737 (tpp) REVERT: B 87 LEU cc_start: 0.9413 (tp) cc_final: 0.9186 (tp) REVERT: B 89 ASN cc_start: 0.9327 (t0) cc_final: 0.8951 (t0) REVERT: C 8 MET cc_start: 0.7718 (tpt) cc_final: 0.7302 (tpp) REVERT: C 23 ASP cc_start: 0.8201 (m-30) cc_final: 0.7930 (p0) REVERT: C 52 THR cc_start: 0.8380 (t) cc_final: 0.7644 (t) REVERT: F 24 PHE cc_start: 0.8627 (m-80) cc_final: 0.8349 (m-80) REVERT: F 29 LEU cc_start: 0.8778 (mm) cc_final: 0.8561 (mm) REVERT: F 47 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7641 (mptt) REVERT: F 84 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8450 (ptp-110) REVERT: F 165 LEU cc_start: 0.9378 (tp) cc_final: 0.8740 (tp) REVERT: F 184 VAL cc_start: 0.8300 (p) cc_final: 0.8091 (p) REVERT: F 207 GLU cc_start: 0.8362 (mp0) cc_final: 0.7906 (mp0) REVERT: F 261 TYR cc_start: 0.6252 (t80) cc_final: 0.5850 (t80) REVERT: G 26 ASN cc_start: 0.7697 (t0) cc_final: 0.7461 (m-40) REVERT: G 40 MET cc_start: 0.8444 (mpp) cc_final: 0.8147 (mpp) REVERT: G 103 PHE cc_start: 0.8059 (t80) cc_final: 0.7639 (t80) REVERT: G 115 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8511 (pm20) REVERT: G 127 MET cc_start: 0.8303 (ptp) cc_final: 0.7921 (ptp) REVERT: E 119 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7090 (tm-30) REVERT: E 123 MET cc_start: 0.8200 (mtp) cc_final: 0.7965 (mtm) REVERT: E 135 MET cc_start: 0.8261 (mtm) cc_final: 0.8044 (mtm) REVERT: E 158 LEU cc_start: 0.9572 (mt) cc_final: 0.9371 (mm) REVERT: E 178 LYS cc_start: 0.8816 (tppt) cc_final: 0.8582 (mmmm) REVERT: E 185 PHE cc_start: 0.8076 (t80) cc_final: 0.7766 (t80) REVERT: E 205 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8307 (ptmt) REVERT: E 219 PHE cc_start: 0.8900 (t80) cc_final: 0.8680 (t80) REVERT: E 223 ASP cc_start: 0.8473 (t0) cc_final: 0.7698 (t70) REVERT: H 47 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8748 (tp40) REVERT: H 54 LEU cc_start: 0.8893 (mt) cc_final: 0.8348 (mt) REVERT: H 58 ILE cc_start: 0.9390 (pt) cc_final: 0.9157 (tp) REVERT: H 134 MET cc_start: 0.7786 (ptm) cc_final: 0.6625 (ppp) REVERT: H 149 TRP cc_start: 0.8650 (m100) cc_final: 0.8245 (m-10) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.2896 time to fit residues: 257.2765 Evaluate side-chains 395 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 149 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 GLN I 115 ASN L 135 GLN B 75 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 75 GLN F 105 ASN G 7 ASN G 105 ASN G 113 HIS ** G 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.086915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064891 restraints weight = 64115.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066732 restraints weight = 41185.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068031 restraints weight = 29311.263| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15161 Z= 0.243 Angle : 0.795 10.362 20629 Z= 0.393 Chirality : 0.045 0.166 2521 Planarity : 0.005 0.058 2568 Dihedral : 8.534 161.589 2121 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.13 % Allowed : 7.87 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.16), residues: 1934 helix: -3.26 (0.14), residues: 681 sheet: -2.94 (0.28), residues: 251 loop : -2.59 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 216 HIS 0.011 0.002 HIS F 226 PHE 0.034 0.002 PHE A 150 TYR 0.024 0.002 TYR D 40 ARG 0.017 0.001 ARG L 102 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 361) hydrogen bonds : angle 5.73756 ( 1032) covalent geometry : bond 0.00498 (15161) covalent geometry : angle 0.79522 (20629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7414 (mp10) cc_final: 0.7208 (mp10) REVERT: A 84 LEU cc_start: 0.7225 (pt) cc_final: 0.6265 (tt) REVERT: A 138 LYS cc_start: 0.8141 (tttt) cc_final: 0.7580 (tppt) REVERT: A 141 MET cc_start: 0.7756 (mmt) cc_final: 0.7519 (tpt) REVERT: D 95 ASP cc_start: 0.5746 (m-30) cc_final: 0.4717 (t0) REVERT: I 13 PHE cc_start: 0.8876 (t80) cc_final: 0.8638 (t80) REVERT: I 138 LYS cc_start: 0.9006 (tptp) cc_final: 0.8728 (mppt) REVERT: I 150 PHE cc_start: 0.7355 (m-80) cc_final: 0.6961 (m-80) REVERT: J 4 LYS cc_start: 0.7937 (tppt) cc_final: 0.7342 (tttt) REVERT: J 5 LYS cc_start: 0.5905 (mptt) cc_final: 0.5651 (mmtp) REVERT: J 92 HIS cc_start: 0.8170 (m90) cc_final: 0.7816 (m-70) REVERT: J 102 ARG cc_start: 0.8803 (mtt180) cc_final: 0.8576 (ttm170) REVERT: J 111 TYR cc_start: 0.8660 (p90) cc_final: 0.8036 (p90) REVERT: J 138 LYS cc_start: 0.7493 (mmtt) cc_final: 0.6701 (tptp) REVERT: L 85 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7402 (mp0) REVERT: L 102 ARG cc_start: 0.9059 (mmt180) cc_final: 0.8380 (mtp85) REVERT: L 135 GLN cc_start: 0.7795 (mm110) cc_final: 0.7333 (pm20) REVERT: B 60 HIS cc_start: 0.8361 (m-70) cc_final: 0.8152 (m-70) REVERT: C 16 LEU cc_start: 0.9123 (mt) cc_final: 0.8775 (mt) REVERT: C 23 ASP cc_start: 0.8442 (m-30) cc_final: 0.8165 (p0) REVERT: C 52 THR cc_start: 0.8543 (t) cc_final: 0.8293 (t) REVERT: F 47 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8120 (mppt) REVERT: F 85 LYS cc_start: 0.8890 (pttt) cc_final: 0.8642 (ptpp) REVERT: F 130 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7564 (mt-10) REVERT: F 183 LEU cc_start: 0.9517 (mp) cc_final: 0.9313 (mm) REVERT: G 40 MET cc_start: 0.8378 (mpp) cc_final: 0.7750 (mpp) REVERT: G 92 GLN cc_start: 0.8440 (pp30) cc_final: 0.8219 (pp30) REVERT: G 101 ASN cc_start: 0.9125 (t0) cc_final: 0.8867 (t0) REVERT: G 126 MET cc_start: 0.8457 (mmm) cc_final: 0.8210 (mmm) REVERT: G 127 MET cc_start: 0.8341 (ptp) cc_final: 0.7785 (ptp) REVERT: G 168 PHE cc_start: 0.8819 (m-80) cc_final: 0.8614 (m-80) REVERT: E 68 MET cc_start: 0.8800 (mtp) cc_final: 0.8203 (mtp) REVERT: E 178 LYS cc_start: 0.9226 (tppt) cc_final: 0.9019 (mmtp) REVERT: E 205 LYS cc_start: 0.9031 (ptpt) cc_final: 0.8720 (ptmt) REVERT: E 223 ASP cc_start: 0.8329 (t0) cc_final: 0.7237 (t70) REVERT: H 29 ASN cc_start: 0.9144 (m110) cc_final: 0.8709 (m110) REVERT: H 54 LEU cc_start: 0.9074 (mt) cc_final: 0.8826 (mt) REVERT: H 127 GLU cc_start: 0.8563 (mp0) cc_final: 0.8113 (mp0) REVERT: H 149 TRP cc_start: 0.8807 (m100) cc_final: 0.8229 (m-10) REVERT: H 201 ASN cc_start: 0.8288 (t0) cc_final: 0.8009 (t0) REVERT: H 205 LYS cc_start: 0.9100 (pttm) cc_final: 0.8743 (pttp) REVERT: H 220 ASN cc_start: 0.9283 (m-40) cc_final: 0.8886 (m-40) outliers start: 2 outliers final: 1 residues processed: 432 average time/residue: 0.2732 time to fit residues: 170.9486 Evaluate side-chains 327 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 92 HIS K 48 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN G 175 GLN ** G 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.088254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066724 restraints weight = 61044.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068546 restraints weight = 39535.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069832 restraints weight = 28331.700| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 15161 Z= 0.106 Angle : 0.627 10.260 20629 Z= 0.294 Chirality : 0.043 0.222 2521 Planarity : 0.004 0.064 2568 Dihedral : 7.963 139.557 2121 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.17), residues: 1934 helix: -2.12 (0.18), residues: 673 sheet: -2.79 (0.29), residues: 242 loop : -2.39 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 7 HIS 0.006 0.001 HIS C 60 PHE 0.020 0.001 PHE F 254 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 361) hydrogen bonds : angle 4.95732 ( 1032) covalent geometry : bond 0.00238 (15161) covalent geometry : angle 0.62708 (20629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 435 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7171 (pt) cc_final: 0.6323 (tt) REVERT: A 138 LYS cc_start: 0.8161 (tttt) cc_final: 0.7558 (tppt) REVERT: A 141 MET cc_start: 0.7782 (mmt) cc_final: 0.7521 (tpt) REVERT: D 95 ASP cc_start: 0.5658 (m-30) cc_final: 0.4651 (t0) REVERT: D 144 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8213 (mt-10) REVERT: I 7 GLU cc_start: 0.9050 (pt0) cc_final: 0.7505 (tm-30) REVERT: I 13 PHE cc_start: 0.8843 (t80) cc_final: 0.8636 (t80) REVERT: I 111 TYR cc_start: 0.9134 (p90) cc_final: 0.8869 (p90) REVERT: I 138 LYS cc_start: 0.8979 (tptp) cc_final: 0.8625 (mmtm) REVERT: I 150 PHE cc_start: 0.7286 (m-80) cc_final: 0.6912 (m-80) REVERT: J 4 LYS cc_start: 0.7901 (tppt) cc_final: 0.7347 (tttt) REVERT: J 92 HIS cc_start: 0.8058 (m90) cc_final: 0.7681 (m-70) REVERT: J 102 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8570 (ttm110) REVERT: J 138 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6453 (tptp) REVERT: L 85 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7529 (mp0) REVERT: L 102 ARG cc_start: 0.9200 (mmt180) cc_final: 0.8763 (mmm-85) REVERT: L 107 LEU cc_start: 0.7564 (tp) cc_final: 0.6960 (pt) REVERT: B 60 HIS cc_start: 0.8151 (m-70) cc_final: 0.7862 (m-70) REVERT: B 88 TYR cc_start: 0.8941 (m-80) cc_final: 0.8698 (m-10) REVERT: C 23 ASP cc_start: 0.8612 (m-30) cc_final: 0.8089 (p0) REVERT: C 52 THR cc_start: 0.8523 (t) cc_final: 0.8153 (t) REVERT: F 29 LEU cc_start: 0.8720 (mm) cc_final: 0.7967 (mm) REVERT: F 47 LYS cc_start: 0.8485 (mmmm) cc_final: 0.7945 (mppt) REVERT: F 130 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7231 (tp30) REVERT: F 139 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7348 (mmmt) REVERT: G 40 MET cc_start: 0.8343 (mpp) cc_final: 0.7804 (mpp) REVERT: G 75 MET cc_start: 0.6608 (ptt) cc_final: 0.6321 (ptt) REVERT: G 90 LEU cc_start: 0.9478 (pp) cc_final: 0.8891 (pp) REVERT: G 98 THR cc_start: 0.9013 (p) cc_final: 0.8626 (t) REVERT: G 101 ASN cc_start: 0.9149 (t0) cc_final: 0.8748 (t0) REVERT: G 104 ASP cc_start: 0.8839 (m-30) cc_final: 0.8384 (m-30) REVERT: G 127 MET cc_start: 0.8260 (ptp) cc_final: 0.7691 (ptp) REVERT: E 46 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8427 (tpm170) REVERT: E 68 MET cc_start: 0.8634 (mtp) cc_final: 0.8280 (mtp) REVERT: E 127 GLU cc_start: 0.8656 (tp30) cc_final: 0.8174 (tp30) REVERT: E 133 GLU cc_start: 0.8848 (pp20) cc_final: 0.8499 (tm-30) REVERT: E 178 LYS cc_start: 0.9177 (tppt) cc_final: 0.8889 (mmmm) REVERT: E 223 ASP cc_start: 0.8158 (t0) cc_final: 0.7435 (t70) REVERT: H 54 LEU cc_start: 0.9024 (mt) cc_final: 0.8789 (mt) REVERT: H 127 GLU cc_start: 0.8443 (mp0) cc_final: 0.8018 (mp0) REVERT: H 149 TRP cc_start: 0.8780 (m100) cc_final: 0.8227 (m-10) REVERT: H 201 ASN cc_start: 0.8166 (t0) cc_final: 0.7865 (t0) REVERT: H 205 LYS cc_start: 0.9047 (pttm) cc_final: 0.8337 (pttm) REVERT: H 220 ASN cc_start: 0.9130 (m-40) cc_final: 0.8656 (m-40) outliers start: 2 outliers final: 0 residues processed: 435 average time/residue: 0.2603 time to fit residues: 164.9491 Evaluate side-chains 339 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 77 optimal weight: 4.9990 chunk 166 optimal weight: 0.0030 chunk 121 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 57 optimal weight: 0.0030 chunk 35 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 135 GLN C 68 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 113 HIS H 73 GLN H 220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.088428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066268 restraints weight = 61710.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068120 restraints weight = 39866.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069444 restraints weight = 28554.669| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15161 Z= 0.098 Angle : 0.620 9.980 20629 Z= 0.287 Chirality : 0.042 0.164 2521 Planarity : 0.004 0.050 2568 Dihedral : 7.399 142.946 2121 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.18), residues: 1934 helix: -1.54 (0.19), residues: 684 sheet: -2.60 (0.29), residues: 243 loop : -2.28 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 216 HIS 0.006 0.001 HIS C 60 PHE 0.026 0.001 PHE H 209 TYR 0.017 0.001 TYR H 222 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 361) hydrogen bonds : angle 4.54699 ( 1032) covalent geometry : bond 0.00220 (15161) covalent geometry : angle 0.61952 (20629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7242 (pt) cc_final: 0.6633 (tt) REVERT: A 138 LYS cc_start: 0.8024 (tttt) cc_final: 0.7495 (tppt) REVERT: D 95 ASP cc_start: 0.5765 (m-30) cc_final: 0.4711 (t0) REVERT: D 144 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8282 (mt-10) REVERT: I 7 GLU cc_start: 0.9074 (pt0) cc_final: 0.7545 (tm-30) REVERT: I 13 PHE cc_start: 0.8839 (t80) cc_final: 0.8627 (t80) REVERT: I 111 TYR cc_start: 0.9102 (p90) cc_final: 0.8775 (p90) REVERT: I 138 LYS cc_start: 0.8932 (tptp) cc_final: 0.8626 (mmtm) REVERT: I 150 PHE cc_start: 0.7226 (m-80) cc_final: 0.6862 (m-80) REVERT: J 4 LYS cc_start: 0.7900 (tppt) cc_final: 0.7329 (tttt) REVERT: J 92 HIS cc_start: 0.8024 (m90) cc_final: 0.7654 (m-70) REVERT: J 111 TYR cc_start: 0.8619 (p90) cc_final: 0.8402 (p90) REVERT: J 138 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6449 (tptp) REVERT: K 48 ASN cc_start: 0.8761 (t0) cc_final: 0.7625 (p0) REVERT: L 85 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7533 (mp0) REVERT: L 102 ARG cc_start: 0.9207 (mmt180) cc_final: 0.8849 (mmm-85) REVERT: L 107 LEU cc_start: 0.7599 (tp) cc_final: 0.7011 (pt) REVERT: B 60 HIS cc_start: 0.8119 (m-70) cc_final: 0.7865 (m-70) REVERT: B 88 TYR cc_start: 0.8823 (m-80) cc_final: 0.8544 (m-10) REVERT: C 23 ASP cc_start: 0.8699 (m-30) cc_final: 0.8107 (p0) REVERT: C 52 THR cc_start: 0.8620 (t) cc_final: 0.8323 (t) REVERT: F 47 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7923 (mppt) REVERT: F 130 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7233 (tp30) REVERT: F 180 MET cc_start: 0.8836 (mmp) cc_final: 0.8287 (mmt) REVERT: G 40 MET cc_start: 0.8235 (mpp) cc_final: 0.7659 (mpp) REVERT: G 75 MET cc_start: 0.6683 (ptt) cc_final: 0.5194 (ptt) REVERT: G 90 LEU cc_start: 0.9384 (pp) cc_final: 0.8707 (pp) REVERT: G 98 THR cc_start: 0.9036 (p) cc_final: 0.8627 (t) REVERT: G 127 MET cc_start: 0.8204 (ptp) cc_final: 0.7653 (ptp) REVERT: G 169 ASP cc_start: 0.8780 (t0) cc_final: 0.8194 (t0) REVERT: E 46 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8385 (tpm170) REVERT: E 68 MET cc_start: 0.8665 (mtp) cc_final: 0.8328 (mtp) REVERT: E 127 GLU cc_start: 0.8563 (tp30) cc_final: 0.8207 (tp30) REVERT: E 133 GLU cc_start: 0.8910 (pp20) cc_final: 0.8539 (tm-30) REVERT: E 178 LYS cc_start: 0.9164 (tppt) cc_final: 0.8803 (mmtp) REVERT: E 223 ASP cc_start: 0.8093 (t0) cc_final: 0.7393 (t70) REVERT: H 54 LEU cc_start: 0.8999 (mt) cc_final: 0.8762 (mt) REVERT: H 72 LEU cc_start: 0.9557 (mm) cc_final: 0.9288 (mm) REVERT: H 127 GLU cc_start: 0.8434 (mp0) cc_final: 0.7928 (mp0) REVERT: H 149 TRP cc_start: 0.8768 (m100) cc_final: 0.8231 (m-10) REVERT: H 201 ASN cc_start: 0.8215 (t0) cc_final: 0.7912 (t0) REVERT: H 205 LYS cc_start: 0.9008 (pttm) cc_final: 0.8503 (pttm) REVERT: H 220 ASN cc_start: 0.9081 (m110) cc_final: 0.8702 (m-40) REVERT: H 223 ASP cc_start: 0.8564 (t70) cc_final: 0.8194 (t0) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.2561 time to fit residues: 158.9522 Evaluate side-chains 338 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 156 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 HIS ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN F 105 ASN F 214 HIS F 226 HIS H 47 GLN H 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.083807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061354 restraints weight = 64867.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063265 restraints weight = 40013.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064572 restraints weight = 27792.208| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15161 Z= 0.167 Angle : 0.668 7.845 20629 Z= 0.323 Chirality : 0.044 0.145 2521 Planarity : 0.004 0.057 2568 Dihedral : 7.116 137.014 2121 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.19), residues: 1934 helix: -0.90 (0.20), residues: 693 sheet: -2.42 (0.31), residues: 241 loop : -2.04 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 29 HIS 0.006 0.001 HIS C 60 PHE 0.017 0.002 PHE H 209 TYR 0.016 0.001 TYR H 222 ARG 0.005 0.001 ARG G 79 Details of bonding type rmsd hydrogen bonds : bond 0.02666 ( 361) hydrogen bonds : angle 4.48596 ( 1032) covalent geometry : bond 0.00368 (15161) covalent geometry : angle 0.66802 (20629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 84 LEU cc_start: 0.7694 (pt) cc_final: 0.6733 (tt) REVERT: A 112 LEU cc_start: 0.8369 (mm) cc_final: 0.8082 (mm) REVERT: A 138 LYS cc_start: 0.8092 (tttt) cc_final: 0.7551 (tppt) REVERT: D 95 ASP cc_start: 0.5702 (m-30) cc_final: 0.4773 (t0) REVERT: D 144 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8264 (mt-10) REVERT: I 7 GLU cc_start: 0.9174 (pt0) cc_final: 0.7682 (tm-30) REVERT: I 111 TYR cc_start: 0.9133 (p90) cc_final: 0.8686 (p90) REVERT: I 138 LYS cc_start: 0.9093 (tptp) cc_final: 0.8866 (tppt) REVERT: I 150 PHE cc_start: 0.7368 (m-80) cc_final: 0.6967 (m-80) REVERT: J 4 LYS cc_start: 0.8118 (tppt) cc_final: 0.7598 (tttt) REVERT: J 92 HIS cc_start: 0.8167 (m90) cc_final: 0.7781 (m-70) REVERT: J 138 LYS cc_start: 0.7463 (mmtt) cc_final: 0.6748 (tptp) REVERT: K 48 ASN cc_start: 0.8761 (t0) cc_final: 0.7786 (p0) REVERT: L 85 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7631 (mp0) REVERT: L 107 LEU cc_start: 0.7695 (tp) cc_final: 0.7124 (pt) REVERT: B 60 HIS cc_start: 0.8369 (m-70) cc_final: 0.7919 (m-70) REVERT: B 88 TYR cc_start: 0.9042 (m-80) cc_final: 0.8779 (m-10) REVERT: C 8 MET cc_start: 0.8173 (tpt) cc_final: 0.7944 (tpp) REVERT: C 23 ASP cc_start: 0.8729 (m-30) cc_final: 0.8267 (p0) REVERT: C 60 HIS cc_start: 0.8470 (m-70) cc_final: 0.8217 (m-70) REVERT: F 29 LEU cc_start: 0.8479 (mm) cc_final: 0.8162 (mm) REVERT: F 47 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8449 (mppt) REVERT: F 89 MET cc_start: 0.8863 (ppp) cc_final: 0.8463 (ppp) REVERT: F 130 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7594 (tp30) REVERT: F 180 MET cc_start: 0.8915 (mmp) cc_final: 0.8439 (mmt) REVERT: G 40 MET cc_start: 0.8373 (mpp) cc_final: 0.7809 (mpp) REVERT: G 90 LEU cc_start: 0.9362 (pp) cc_final: 0.8637 (pp) REVERT: G 98 THR cc_start: 0.9142 (p) cc_final: 0.8747 (t) REVERT: G 127 MET cc_start: 0.8351 (ptp) cc_final: 0.7822 (ptp) REVERT: G 169 ASP cc_start: 0.8773 (t0) cc_final: 0.8516 (t0) REVERT: E 68 MET cc_start: 0.8687 (mtp) cc_final: 0.8247 (mtp) REVERT: E 127 GLU cc_start: 0.8693 (tp30) cc_final: 0.8074 (tp30) REVERT: E 133 GLU cc_start: 0.9079 (pp20) cc_final: 0.8726 (tm-30) REVERT: E 178 LYS cc_start: 0.9282 (tppt) cc_final: 0.8917 (mmtt) REVERT: E 180 ILE cc_start: 0.8723 (pt) cc_final: 0.8309 (pt) REVERT: E 207 VAL cc_start: 0.9654 (m) cc_final: 0.9379 (p) REVERT: E 223 ASP cc_start: 0.8262 (t0) cc_final: 0.7621 (t70) REVERT: H 54 LEU cc_start: 0.9061 (mt) cc_final: 0.8756 (mt) REVERT: H 56 MET cc_start: 0.8532 (tpp) cc_final: 0.8092 (tmm) REVERT: H 127 GLU cc_start: 0.8499 (mp0) cc_final: 0.7961 (mp0) REVERT: H 201 ASN cc_start: 0.8465 (t0) cc_final: 0.8090 (t0) REVERT: H 220 ASN cc_start: 0.9242 (m-40) cc_final: 0.8780 (m-40) REVERT: H 223 ASP cc_start: 0.8730 (t70) cc_final: 0.8323 (t0) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.2617 time to fit residues: 158.9335 Evaluate side-chains 329 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 0.0970 chunk 136 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 153 optimal weight: 0.0570 chunk 183 optimal weight: 7.9990 chunk 123 optimal weight: 0.0570 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 ASN H 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064026 restraints weight = 63488.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065828 restraints weight = 41524.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067038 restraints weight = 29970.048| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15161 Z= 0.098 Angle : 0.639 8.995 20629 Z= 0.294 Chirality : 0.043 0.191 2521 Planarity : 0.004 0.051 2568 Dihedral : 6.657 138.997 2121 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1934 helix: -0.76 (0.20), residues: 699 sheet: -2.27 (0.31), residues: 241 loop : -2.04 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 29 HIS 0.005 0.001 HIS C 60 PHE 0.020 0.001 PHE I 13 TYR 0.019 0.001 TYR H 222 ARG 0.006 0.000 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.02227 ( 361) hydrogen bonds : angle 4.23418 ( 1032) covalent geometry : bond 0.00223 (15161) covalent geometry : angle 0.63933 (20629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7543 (mp10) cc_final: 0.7295 (tp-100) REVERT: A 84 LEU cc_start: 0.7703 (pt) cc_final: 0.6758 (tt) REVERT: A 112 LEU cc_start: 0.8289 (mm) cc_final: 0.8014 (mm) REVERT: A 138 LYS cc_start: 0.8075 (tttt) cc_final: 0.7543 (tppt) REVERT: D 67 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8121 (tpp80) REVERT: D 95 ASP cc_start: 0.5707 (m-30) cc_final: 0.4732 (t0) REVERT: I 7 GLU cc_start: 0.9026 (pt0) cc_final: 0.7584 (tm-30) REVERT: I 18 LEU cc_start: 0.9190 (tt) cc_final: 0.8970 (mt) REVERT: I 111 TYR cc_start: 0.9074 (p90) cc_final: 0.8625 (p90) REVERT: I 138 LYS cc_start: 0.9079 (tptp) cc_final: 0.8722 (mmtm) REVERT: I 150 PHE cc_start: 0.7328 (m-10) cc_final: 0.6996 (m-80) REVERT: J 4 LYS cc_start: 0.8112 (tppt) cc_final: 0.7602 (tttt) REVERT: J 92 HIS cc_start: 0.8073 (m90) cc_final: 0.7687 (m-70) REVERT: J 138 LYS cc_start: 0.7439 (mmtt) cc_final: 0.6708 (tptp) REVERT: K 48 ASN cc_start: 0.8651 (t0) cc_final: 0.7646 (p0) REVERT: K 53 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8107 (mmtt) REVERT: L 85 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7661 (mp0) REVERT: L 107 LEU cc_start: 0.7775 (tp) cc_final: 0.7175 (pt) REVERT: L 114 LEU cc_start: 0.7862 (mm) cc_final: 0.7428 (mm) REVERT: B 60 HIS cc_start: 0.8006 (m-70) cc_final: 0.7610 (m-70) REVERT: B 88 TYR cc_start: 0.8784 (m-80) cc_final: 0.8558 (m-10) REVERT: C 8 MET cc_start: 0.8055 (tpt) cc_final: 0.7803 (tpp) REVERT: C 23 ASP cc_start: 0.8532 (m-30) cc_final: 0.8112 (p0) REVERT: C 60 HIS cc_start: 0.8387 (m-70) cc_final: 0.8093 (m-70) REVERT: F 29 LEU cc_start: 0.8447 (mm) cc_final: 0.8023 (mm) REVERT: F 47 LYS cc_start: 0.8578 (mmmm) cc_final: 0.8255 (mppt) REVERT: F 130 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7361 (tp30) REVERT: F 180 MET cc_start: 0.8766 (mmp) cc_final: 0.8366 (mmt) REVERT: G 40 MET cc_start: 0.8130 (mpp) cc_final: 0.7838 (mpp) REVERT: G 90 LEU cc_start: 0.9353 (pp) cc_final: 0.8848 (pp) REVERT: G 98 THR cc_start: 0.9046 (p) cc_final: 0.8648 (t) REVERT: G 127 MET cc_start: 0.8395 (ptp) cc_final: 0.7979 (ptp) REVERT: G 134 LEU cc_start: 0.9418 (mt) cc_final: 0.9166 (mm) REVERT: E 46 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8400 (tpm170) REVERT: E 68 MET cc_start: 0.8495 (mtp) cc_final: 0.8069 (mtp) REVERT: E 127 GLU cc_start: 0.8429 (tp30) cc_final: 0.8007 (tp30) REVERT: E 133 GLU cc_start: 0.8988 (pp20) cc_final: 0.8649 (tm-30) REVERT: E 180 ILE cc_start: 0.8719 (pt) cc_final: 0.8300 (pt) REVERT: E 223 ASP cc_start: 0.8012 (t0) cc_final: 0.7349 (t70) REVERT: E 257 MET cc_start: 0.5579 (mtt) cc_final: 0.4041 (mmm) REVERT: H 56 MET cc_start: 0.8280 (tpp) cc_final: 0.8039 (tmm) REVERT: H 127 GLU cc_start: 0.8438 (mp0) cc_final: 0.7842 (mp0) REVERT: H 149 TRP cc_start: 0.8836 (m100) cc_final: 0.8197 (m-10) REVERT: H 220 ASN cc_start: 0.9017 (m110) cc_final: 0.8574 (m-40) REVERT: H 223 ASP cc_start: 0.8578 (t70) cc_final: 0.8205 (t0) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.3056 time to fit residues: 197.2820 Evaluate side-chains 349 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 47 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 ASN H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.083575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061739 restraints weight = 63954.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063471 restraints weight = 40379.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064712 restraints weight = 28797.102| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15161 Z= 0.126 Angle : 0.654 8.675 20629 Z= 0.305 Chirality : 0.043 0.162 2521 Planarity : 0.004 0.048 2568 Dihedral : 6.419 156.266 2121 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.19), residues: 1934 helix: -0.43 (0.21), residues: 704 sheet: -2.19 (0.30), residues: 269 loop : -1.94 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 7 HIS 0.004 0.001 HIS C 60 PHE 0.022 0.001 PHE F 168 TYR 0.011 0.001 TYR F 261 ARG 0.004 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02361 ( 361) hydrogen bonds : angle 4.22991 ( 1032) covalent geometry : bond 0.00287 (15161) covalent geometry : angle 0.65376 (20629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7731 (pt) cc_final: 0.6809 (tt) REVERT: A 112 LEU cc_start: 0.8301 (mm) cc_final: 0.8021 (mm) REVERT: A 138 LYS cc_start: 0.8068 (tttt) cc_final: 0.7486 (tptp) REVERT: D 67 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8291 (ttm110) REVERT: D 95 ASP cc_start: 0.5595 (m-30) cc_final: 0.4730 (t0) REVERT: D 144 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8481 (mt-10) REVERT: I 111 TYR cc_start: 0.9106 (p90) cc_final: 0.8583 (p90) REVERT: I 138 LYS cc_start: 0.9064 (tptp) cc_final: 0.8840 (tppt) REVERT: I 150 PHE cc_start: 0.7390 (m-10) cc_final: 0.7036 (m-80) REVERT: J 4 LYS cc_start: 0.8142 (tppt) cc_final: 0.7629 (tttt) REVERT: J 92 HIS cc_start: 0.8130 (m90) cc_final: 0.7736 (m-70) REVERT: J 138 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6664 (tptp) REVERT: K 48 ASN cc_start: 0.8707 (t0) cc_final: 0.7764 (p0) REVERT: K 53 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8236 (mmtt) REVERT: L 85 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7715 (mp0) REVERT: L 107 LEU cc_start: 0.7771 (tp) cc_final: 0.7188 (pt) REVERT: L 114 LEU cc_start: 0.7935 (mm) cc_final: 0.7508 (mm) REVERT: L 146 LEU cc_start: 0.8723 (mt) cc_final: 0.8374 (mt) REVERT: B 60 HIS cc_start: 0.8222 (m-70) cc_final: 0.7806 (m-70) REVERT: B 88 TYR cc_start: 0.8947 (m-80) cc_final: 0.8702 (m-10) REVERT: C 23 ASP cc_start: 0.8705 (m-30) cc_final: 0.8175 (p0) REVERT: C 60 HIS cc_start: 0.8543 (m-70) cc_final: 0.8210 (m-70) REVERT: F 29 LEU cc_start: 0.8498 (mm) cc_final: 0.8141 (mm) REVERT: F 47 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8551 (mppt) REVERT: F 89 MET cc_start: 0.8707 (ppp) cc_final: 0.8369 (ppp) REVERT: F 130 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7616 (tp30) REVERT: F 180 MET cc_start: 0.8887 (mmp) cc_final: 0.8328 (mmt) REVERT: G 35 LYS cc_start: 0.9112 (mptt) cc_final: 0.8804 (mmmt) REVERT: G 40 MET cc_start: 0.8173 (mpp) cc_final: 0.7971 (mpp) REVERT: G 90 LEU cc_start: 0.9351 (pp) cc_final: 0.8788 (pp) REVERT: G 127 MET cc_start: 0.8539 (ptp) cc_final: 0.8045 (ptp) REVERT: G 169 ASP cc_start: 0.8673 (t0) cc_final: 0.8378 (t70) REVERT: E 56 MET cc_start: 0.8249 (mmm) cc_final: 0.7838 (mmm) REVERT: E 68 MET cc_start: 0.8639 (mtp) cc_final: 0.8254 (mtp) REVERT: E 127 GLU cc_start: 0.8477 (tp30) cc_final: 0.7931 (tp30) REVERT: E 133 GLU cc_start: 0.9019 (pp20) cc_final: 0.8728 (tm-30) REVERT: E 178 LYS cc_start: 0.9208 (tppt) cc_final: 0.8846 (mmtt) REVERT: E 223 ASP cc_start: 0.8106 (t0) cc_final: 0.7463 (t70) REVERT: E 257 MET cc_start: 0.5628 (mtt) cc_final: 0.4121 (mmm) REVERT: H 56 MET cc_start: 0.8537 (tpp) cc_final: 0.8111 (tmm) REVERT: H 201 ASN cc_start: 0.8405 (t0) cc_final: 0.8101 (t0) REVERT: H 220 ASN cc_start: 0.9139 (m110) cc_final: 0.8719 (m-40) REVERT: H 223 ASP cc_start: 0.8692 (t70) cc_final: 0.8300 (t0) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.3871 time to fit residues: 244.5536 Evaluate side-chains 329 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 138 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.063770 restraints weight = 62109.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.065450 restraints weight = 41563.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066593 restraints weight = 30383.848| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15161 Z= 0.101 Angle : 0.658 11.989 20629 Z= 0.302 Chirality : 0.043 0.160 2521 Planarity : 0.003 0.044 2568 Dihedral : 6.217 152.980 2121 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.19), residues: 1934 helix: -0.41 (0.20), residues: 714 sheet: -2.13 (0.30), residues: 268 loop : -1.95 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 195 HIS 0.015 0.001 HIS G 203 PHE 0.017 0.001 PHE H 209 TYR 0.012 0.001 TYR H 49 ARG 0.005 0.000 ARG I 67 Details of bonding type rmsd hydrogen bonds : bond 0.02054 ( 361) hydrogen bonds : angle 4.14020 ( 1032) covalent geometry : bond 0.00229 (15161) covalent geometry : angle 0.65754 (20629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7737 (pt) cc_final: 0.6260 (tt) REVERT: A 112 LEU cc_start: 0.8197 (mm) cc_final: 0.7921 (mm) REVERT: A 138 LYS cc_start: 0.8031 (tttt) cc_final: 0.7448 (tptp) REVERT: D 95 ASP cc_start: 0.5723 (m-30) cc_final: 0.4829 (t0) REVERT: I 111 TYR cc_start: 0.9057 (p90) cc_final: 0.8540 (p90) REVERT: I 138 LYS cc_start: 0.9019 (tptp) cc_final: 0.8694 (mmtm) REVERT: I 150 PHE cc_start: 0.7313 (m-10) cc_final: 0.6974 (m-80) REVERT: J 4 LYS cc_start: 0.8145 (tppt) cc_final: 0.7627 (tttt) REVERT: J 92 HIS cc_start: 0.7980 (m90) cc_final: 0.7615 (m-70) REVERT: J 138 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6713 (tptp) REVERT: K 48 ASN cc_start: 0.8649 (t0) cc_final: 0.7697 (p0) REVERT: K 53 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8281 (mmtt) REVERT: L 85 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7775 (mp0) REVERT: L 107 LEU cc_start: 0.7819 (tp) cc_final: 0.7226 (pt) REVERT: L 114 LEU cc_start: 0.7730 (mm) cc_final: 0.7304 (mm) REVERT: B 60 HIS cc_start: 0.7975 (m-70) cc_final: 0.7578 (m-70) REVERT: B 88 TYR cc_start: 0.8756 (m-80) cc_final: 0.8551 (m-10) REVERT: C 23 ASP cc_start: 0.8531 (m-30) cc_final: 0.8078 (p0) REVERT: C 60 HIS cc_start: 0.8517 (m-70) cc_final: 0.8173 (m-70) REVERT: F 29 LEU cc_start: 0.8410 (mm) cc_final: 0.8061 (mm) REVERT: F 47 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8440 (mppt) REVERT: F 130 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7545 (tp30) REVERT: G 35 LYS cc_start: 0.9021 (mptt) cc_final: 0.8755 (mmmt) REVERT: G 90 LEU cc_start: 0.9183 (pp) cc_final: 0.8733 (pp) REVERT: G 127 MET cc_start: 0.8505 (ptp) cc_final: 0.8158 (ptp) REVERT: G 134 LEU cc_start: 0.9427 (mt) cc_final: 0.9163 (mm) REVERT: E 46 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8414 (tpm170) REVERT: E 56 MET cc_start: 0.8090 (mmm) cc_final: 0.7639 (mmm) REVERT: E 68 MET cc_start: 0.8558 (mtp) cc_final: 0.8220 (mtm) REVERT: E 133 GLU cc_start: 0.8906 (pp20) cc_final: 0.8641 (tm-30) REVERT: E 178 LYS cc_start: 0.9159 (tppt) cc_final: 0.8819 (mmtt) REVERT: E 223 ASP cc_start: 0.7935 (t0) cc_final: 0.7290 (t70) REVERT: E 257 MET cc_start: 0.5379 (mtt) cc_final: 0.3984 (mmm) REVERT: H 17 LEU cc_start: 0.9194 (mt) cc_final: 0.8973 (mt) REVERT: H 47 GLN cc_start: 0.9038 (tp40) cc_final: 0.8806 (tp40) REVERT: H 56 MET cc_start: 0.8302 (tpp) cc_final: 0.8017 (tmm) REVERT: H 73 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8448 (mm-40) REVERT: H 89 MET cc_start: 0.8850 (mpp) cc_final: 0.8605 (mmt) REVERT: H 149 TRP cc_start: 0.8837 (m100) cc_final: 0.8050 (m-10) REVERT: H 220 ASN cc_start: 0.9003 (m110) cc_final: 0.8653 (m110) REVERT: H 223 ASP cc_start: 0.8581 (t70) cc_final: 0.8220 (t0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3282 time to fit residues: 204.0307 Evaluate side-chains 336 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 160 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN H 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.083334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060716 restraints weight = 64566.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062611 restraints weight = 39368.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063944 restraints weight = 27382.708| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15161 Z= 0.124 Angle : 0.666 8.478 20629 Z= 0.311 Chirality : 0.043 0.158 2521 Planarity : 0.003 0.047 2568 Dihedral : 6.057 140.557 2121 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.19), residues: 1934 helix: -0.17 (0.21), residues: 706 sheet: -2.07 (0.30), residues: 263 loop : -1.84 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 29 HIS 0.004 0.001 HIS F 113 PHE 0.021 0.001 PHE H 209 TYR 0.010 0.001 TYR D 40 ARG 0.009 0.001 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.02222 ( 361) hydrogen bonds : angle 4.21378 ( 1032) covalent geometry : bond 0.00287 (15161) covalent geometry : angle 0.66648 (20629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7419 (pt) cc_final: 0.6997 (tt) REVERT: A 112 LEU cc_start: 0.8208 (mm) cc_final: 0.7931 (mm) REVERT: A 138 LYS cc_start: 0.8016 (tttt) cc_final: 0.7411 (tptp) REVERT: D 67 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8322 (ttm110) REVERT: D 95 ASP cc_start: 0.5678 (m-30) cc_final: 0.4786 (t0) REVERT: I 111 TYR cc_start: 0.9101 (p90) cc_final: 0.8577 (p90) REVERT: I 150 PHE cc_start: 0.7388 (m-10) cc_final: 0.7022 (m-80) REVERT: J 4 LYS cc_start: 0.8252 (tppt) cc_final: 0.7732 (tttt) REVERT: J 92 HIS cc_start: 0.8140 (m90) cc_final: 0.7728 (m-70) REVERT: J 138 LYS cc_start: 0.7475 (mmtt) cc_final: 0.6860 (tptp) REVERT: K 48 ASN cc_start: 0.8771 (t0) cc_final: 0.7975 (p0) REVERT: K 53 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8423 (mmtt) REVERT: L 85 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7288 (mp0) REVERT: L 107 LEU cc_start: 0.7774 (tp) cc_final: 0.7234 (pt) REVERT: L 114 LEU cc_start: 0.7974 (mm) cc_final: 0.7546 (mm) REVERT: B 60 HIS cc_start: 0.8327 (m-70) cc_final: 0.7834 (m-70) REVERT: C 23 ASP cc_start: 0.8798 (m-30) cc_final: 0.8234 (p0) REVERT: C 60 HIS cc_start: 0.8698 (m-70) cc_final: 0.8178 (m-70) REVERT: F 29 LEU cc_start: 0.8551 (mm) cc_final: 0.8179 (mm) REVERT: F 40 MET cc_start: 0.8412 (mmp) cc_final: 0.7914 (mmt) REVERT: F 47 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8634 (mppt) REVERT: F 89 MET cc_start: 0.8987 (ppp) cc_final: 0.8432 (ppp) REVERT: F 113 HIS cc_start: 0.8021 (m-70) cc_final: 0.7138 (m-70) REVERT: F 130 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7811 (tp30) REVERT: F 180 MET cc_start: 0.9022 (mmt) cc_final: 0.8310 (mmm) REVERT: G 35 LYS cc_start: 0.9193 (mptt) cc_final: 0.8841 (mmmt) REVERT: G 127 MET cc_start: 0.8722 (ptp) cc_final: 0.8350 (ptp) REVERT: G 203 HIS cc_start: 0.8878 (p-80) cc_final: 0.8398 (p-80) REVERT: E 56 MET cc_start: 0.8601 (mmm) cc_final: 0.8170 (mmm) REVERT: E 68 MET cc_start: 0.8784 (mtp) cc_final: 0.8478 (mtm) REVERT: E 98 GLU cc_start: 0.7757 (pm20) cc_final: 0.7483 (pm20) REVERT: E 133 GLU cc_start: 0.8968 (pp20) cc_final: 0.8752 (tm-30) REVERT: E 178 LYS cc_start: 0.9280 (tppt) cc_final: 0.8943 (mmtt) REVERT: E 223 ASP cc_start: 0.8197 (t0) cc_final: 0.7640 (t70) REVERT: E 257 MET cc_start: 0.5420 (mtt) cc_final: 0.4173 (mmm) REVERT: H 17 LEU cc_start: 0.9234 (mt) cc_final: 0.9011 (mt) REVERT: H 56 MET cc_start: 0.8416 (tpp) cc_final: 0.8103 (tmm) REVERT: H 73 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8491 (mm-40) REVERT: H 220 ASN cc_start: 0.9288 (m-40) cc_final: 0.8890 (m-40) REVERT: H 223 ASP cc_start: 0.8764 (t70) cc_final: 0.8361 (t0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2612 time to fit residues: 156.0901 Evaluate side-chains 329 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.081909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059767 restraints weight = 65771.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061465 restraints weight = 41510.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062631 restraints weight = 29646.082| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15161 Z= 0.138 Angle : 0.679 8.069 20629 Z= 0.319 Chirality : 0.044 0.157 2521 Planarity : 0.004 0.045 2568 Dihedral : 5.968 133.120 2121 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1934 helix: -0.01 (0.21), residues: 706 sheet: -2.09 (0.30), residues: 263 loop : -1.79 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 7 HIS 0.003 0.001 HIS C 60 PHE 0.039 0.002 PHE G 254 TYR 0.015 0.001 TYR B 88 ARG 0.008 0.001 ARG K 81 Details of bonding type rmsd hydrogen bonds : bond 0.02319 ( 361) hydrogen bonds : angle 4.19764 ( 1032) covalent geometry : bond 0.00311 (15161) covalent geometry : angle 0.67897 (20629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 49 ILE cc_start: 0.9246 (pt) cc_final: 0.9036 (pt) REVERT: A 84 LEU cc_start: 0.7754 (pt) cc_final: 0.6903 (tt) REVERT: A 112 LEU cc_start: 0.8280 (mm) cc_final: 0.7921 (mm) REVERT: A 138 LYS cc_start: 0.8058 (tttt) cc_final: 0.7437 (tptp) REVERT: D 67 ARG cc_start: 0.8528 (ttp-110) cc_final: 0.8235 (ttm110) REVERT: D 84 LEU cc_start: 0.7932 (mp) cc_final: 0.7382 (pp) REVERT: D 95 ASP cc_start: 0.5610 (m-30) cc_final: 0.4794 (t0) REVERT: I 111 TYR cc_start: 0.9099 (p90) cc_final: 0.8489 (p90) REVERT: I 150 PHE cc_start: 0.7437 (m-10) cc_final: 0.7066 (m-80) REVERT: J 4 LYS cc_start: 0.8250 (tppt) cc_final: 0.7779 (tttt) REVERT: J 92 HIS cc_start: 0.8144 (m90) cc_final: 0.7740 (m-70) REVERT: J 138 LYS cc_start: 0.7546 (mmtt) cc_final: 0.6953 (tptp) REVERT: K 48 ASN cc_start: 0.8748 (t0) cc_final: 0.8053 (p0) REVERT: L 85 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7496 (mp0) REVERT: L 107 LEU cc_start: 0.7872 (tp) cc_final: 0.7275 (pt) REVERT: L 114 LEU cc_start: 0.7998 (mm) cc_final: 0.7570 (mm) REVERT: B 60 HIS cc_start: 0.8219 (m-70) cc_final: 0.7721 (m-70) REVERT: C 23 ASP cc_start: 0.8799 (m-30) cc_final: 0.8297 (p0) REVERT: C 60 HIS cc_start: 0.8690 (m-70) cc_final: 0.8083 (m-70) REVERT: C 63 ASP cc_start: 0.8792 (p0) cc_final: 0.7698 (p0) REVERT: F 29 LEU cc_start: 0.8460 (mm) cc_final: 0.8061 (mm) REVERT: F 40 MET cc_start: 0.8311 (mmp) cc_final: 0.7943 (mmt) REVERT: F 47 LYS cc_start: 0.9303 (mmmm) cc_final: 0.8657 (mppt) REVERT: F 89 MET cc_start: 0.9074 (ppp) cc_final: 0.8559 (ppp) REVERT: F 113 HIS cc_start: 0.8189 (m-70) cc_final: 0.7140 (m-70) REVERT: F 130 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7695 (tp30) REVERT: G 35 LYS cc_start: 0.9135 (mptt) cc_final: 0.8829 (mmmt) REVERT: G 87 MET cc_start: 0.8776 (mpp) cc_final: 0.8523 (mpp) REVERT: G 127 MET cc_start: 0.8638 (ptp) cc_final: 0.8266 (ptp) REVERT: G 203 HIS cc_start: 0.8717 (p-80) cc_final: 0.8352 (p-80) REVERT: E 68 MET cc_start: 0.8710 (mtp) cc_final: 0.8486 (mtm) REVERT: E 98 GLU cc_start: 0.7582 (pm20) cc_final: 0.7303 (pm20) REVERT: E 133 GLU cc_start: 0.8907 (pp20) cc_final: 0.8674 (tm-30) REVERT: E 178 LYS cc_start: 0.9244 (tppt) cc_final: 0.8863 (mmmm) REVERT: E 223 ASP cc_start: 0.8054 (t0) cc_final: 0.7418 (t70) REVERT: E 257 MET cc_start: 0.5363 (mtt) cc_final: 0.4230 (mmm) REVERT: H 17 LEU cc_start: 0.9255 (mt) cc_final: 0.9029 (mt) REVERT: H 47 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8887 (tp-100) REVERT: H 73 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8435 (mm-40) REVERT: H 89 MET cc_start: 0.8852 (mpp) cc_final: 0.8580 (mmt) REVERT: H 216 ILE cc_start: 0.9666 (mt) cc_final: 0.9459 (mt) REVERT: H 220 ASN cc_start: 0.9270 (m-40) cc_final: 0.8771 (m-40) REVERT: H 223 ASP cc_start: 0.8660 (t70) cc_final: 0.8289 (t0) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2617 time to fit residues: 158.2617 Evaluate side-chains 333 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 chunk 88 optimal weight: 0.0040 chunk 188 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061178 restraints weight = 64909.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062873 restraints weight = 41228.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064066 restraints weight = 29555.488| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15161 Z= 0.106 Angle : 0.676 9.014 20629 Z= 0.311 Chirality : 0.044 0.154 2521 Planarity : 0.004 0.077 2568 Dihedral : 5.852 127.632 2121 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1934 helix: -0.01 (0.21), residues: 703 sheet: -2.07 (0.30), residues: 263 loop : -1.78 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 7 HIS 0.003 0.001 HIS G 203 PHE 0.034 0.001 PHE G 254 TYR 0.012 0.001 TYR B 88 ARG 0.008 0.000 ARG K 81 Details of bonding type rmsd hydrogen bonds : bond 0.02094 ( 361) hydrogen bonds : angle 4.08809 ( 1032) covalent geometry : bond 0.00250 (15161) covalent geometry : angle 0.67639 (20629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.77 seconds wall clock time: 105 minutes 10.89 seconds (6310.89 seconds total)