Starting phenix.real_space_refine on Sun Jun 22 23:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmi_38478/06_2025/8xmi_38478.cif" } resolution = 3.0 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 115 5.16 5 Na 4 4.78 5 C 17302 2.51 5 N 4377 2.21 5 O 4892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26718 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1582 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 196} Chain breaks: 3 Chain: "E" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1568 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.21, per 1000 atoms: 0.64 Number of scatterers: 26718 At special positions: 0 Unit cell: (178.45, 172.64, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 115 16.00 P 24 15.00 Na 4 11.00 O 4892 8.00 N 4377 7.00 C 17302 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: 6.58 Conformation dependent library (CDL) restraints added in 3.6 seconds 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 23 sheets defined 58.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.836A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.531A pdb=" N PHE A 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.699A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 removed outlier: 3.668A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.542A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 6.149A pdb=" N ARG B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 71 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.517A pdb=" N SER B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.895A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.609A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 66 through 71 removed outlier: 6.177A pdb=" N ARG C 69 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.618A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.651A pdb=" N LEU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.550A pdb=" N SER D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'E' and resid 17 through 28 Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 66 removed outlier: 3.548A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 138 removed outlier: 3.573A pdb=" N SER E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 221 removed outlier: 3.642A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 29 Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 66 through 71 removed outlier: 6.127A pdb=" N ARG F 69 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 138 removed outlier: 3.587A pdb=" N SER F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 221 removed outlier: 3.558A pdb=" N ASN F 219 " --> pdb=" O LYS F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 28 Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 67 removed outlier: 3.729A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'G' and resid 211 through 221 removed outlier: 3.909A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 28 Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.644A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 138 removed outlier: 3.616A pdb=" N SER H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 221 removed outlier: 3.659A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.664A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 103 removed outlier: 4.169A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.785A pdb=" N LEU I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 174 removed outlier: 3.566A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix removed outlier: 7.595A pdb=" N TRP I 158 " --> pdb=" O PRO I 154 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N SER I 159 " --> pdb=" O GLN I 155 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER I 160 " --> pdb=" O TYR I 156 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 162 " --> pdb=" O TRP I 158 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 261 through 275 removed outlier: 3.515A pdb=" N VAL I 274 " --> pdb=" O TYR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 289 removed outlier: 3.564A pdb=" N MET I 289 " --> pdb=" O PHE I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.528A pdb=" N PHE I 296 " --> pdb=" O GLY I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 397 through 401 removed outlier: 3.526A pdb=" N LEU I 401 " --> pdb=" O THR I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 419 removed outlier: 3.509A pdb=" N CYS I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 removed outlier: 4.194A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 37 removed outlier: 3.725A pdb=" N LEU J 20 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 41 removed outlier: 3.716A pdb=" N THR J 41 " --> pdb=" O PRO J 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 38 through 41' Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.522A pdb=" N PHE J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 103 removed outlier: 4.000A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 3.515A pdb=" N LEU J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 157 removed outlier: 4.148A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 160 through 174 Processing helix chain 'J' and resid 191 through 207 Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 250 Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.574A pdb=" N ILE J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 402 through 419 removed outlier: 3.556A pdb=" N CYS J 407 " --> pdb=" O THR J 403 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE J 408 " --> pdb=" O ALA J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 428 removed outlier: 4.022A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 36 removed outlier: 3.624A pdb=" N LEU K 20 " --> pdb=" O PRO K 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.748A pdb=" N PHE K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 103 removed outlier: 3.958A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.844A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 174 removed outlier: 4.212A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix removed outlier: 7.589A pdb=" N TRP K 158 " --> pdb=" O PRO K 154 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N SER K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 160 " --> pdb=" O TYR K 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 208 through 218 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 251 Processing helix chain 'K' and resid 261 through 275 removed outlier: 3.536A pdb=" N VAL K 274 " --> pdb=" O TYR K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.500A pdb=" N SER K 288 " --> pdb=" O ASP K 285 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET K 289 " --> pdb=" O PHE K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 285 through 289' Processing helix chain 'K' and resid 290 through 303 Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 removed outlier: 3.561A pdb=" N ILE K 371 " --> pdb=" O PHE K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 397 through 401 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 428 removed outlier: 4.165A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 37 removed outlier: 3.859A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.041A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 95 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 removed outlier: 3.705A pdb=" N LEU L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 174 removed outlier: 3.601A pdb=" N LEU L 129 " --> pdb=" O GLY L 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix removed outlier: 7.977A pdb=" N TRP L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N SER L 159 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 160 " --> pdb=" O TYR L 156 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 207 Processing helix chain 'L' and resid 208 through 218 removed outlier: 3.614A pdb=" N LYS L 217 " --> pdb=" O PHE L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.502A pdb=" N LEU L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 275 removed outlier: 3.513A pdb=" N VAL L 274 " --> pdb=" O TYR L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 289 Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.565A pdb=" N ILE L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 397 through 401 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 428 removed outlier: 3.556A pdb=" N SER L 426 " --> pdb=" O THR L 422 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.684A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.207A pdb=" N VAL A 141 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 209 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 156 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 183 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A 206 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 166 removed outlier: 4.026A pdb=" N LYS A 165 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.528A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 146 removed outlier: 5.979A pdb=" N VAL B 141 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU B 157 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 143 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 209 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 183 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 206 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.537A pdb=" N VAL C 32 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 53 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA C 34 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE C 9 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 35 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 11 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.349A pdb=" N VAL C 141 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU C 157 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N CYS C 204 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 182 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.618A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.797A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 209 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 206 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 51 through 53 removed outlier: 6.637A pdb=" N GLN E 8 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE E 75 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA E 10 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 143 removed outlier: 6.225A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 143 removed outlier: 6.225A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 182 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.574A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.124A pdb=" N VAL F 141 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU F 157 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N CYS F 204 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE F 183 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL F 206 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.522A pdb=" N VAL G 32 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL G 53 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA G 34 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE G 9 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL G 35 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL G 11 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL G 74 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LYS G 103 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL G 76 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 143 through 146 removed outlier: 4.002A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE G 183 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 206 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.766A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 143 through 146 removed outlier: 3.800A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 183 " --> pdb=" O CYS H 204 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL H 206 " --> pdb=" O LEU H 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 165 through 166 removed outlier: 4.152A pdb=" N LYS H 165 " --> pdb=" O ILE H 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.668A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER I 342 " --> pdb=" O GLY J 440 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.685A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.697A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.568A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1531 hydrogen bonds defined for protein. 4413 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: 9.94 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4633 1.32 - 1.44: 6622 1.44 - 1.57: 15723 1.57 - 1.69: 40 1.69 - 1.81: 195 Bond restraints: 27213 Sorted by residual: bond pdb=" N LEU J 352 " pdb=" CA LEU J 352 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.21e-02 6.83e+03 2.15e+01 bond pdb=" CA THR I 41 " pdb=" C THR I 41 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.20e-02 6.94e+03 1.99e+01 bond pdb=" CA ALA J 351 " pdb=" C ALA J 351 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" CA GLY G 67 " pdb=" C GLY G 67 " ideal model delta sigma weight residual 1.514 1.455 0.059 1.41e-02 5.03e+03 1.77e+01 bond pdb=" N VAL J 354 " pdb=" CA VAL J 354 " ideal model delta sigma weight residual 1.461 1.414 0.047 1.19e-02 7.06e+03 1.54e+01 ... (remaining 27208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 36556 2.32 - 4.64: 323 4.64 - 6.96: 37 6.96 - 9.28: 13 9.28 - 11.61: 1 Bond angle restraints: 36930 Sorted by residual: angle pdb=" N SER J 283 " pdb=" CA SER J 283 " pdb=" C SER J 283 " ideal model delta sigma weight residual 114.31 107.90 6.41 1.29e+00 6.01e-01 2.47e+01 angle pdb=" N GLY G 67 " pdb=" CA GLY G 67 " pdb=" C GLY G 67 " ideal model delta sigma weight residual 113.18 101.57 11.61 2.37e+00 1.78e-01 2.40e+01 angle pdb=" N LEU J 298 " pdb=" CA LEU J 298 " pdb=" C LEU J 298 " ideal model delta sigma weight residual 111.14 106.00 5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N ASN J 282 " pdb=" CA ASN J 282 " pdb=" C ASN J 282 " ideal model delta sigma weight residual 108.79 115.93 -7.14 1.53e+00 4.27e-01 2.18e+01 angle pdb=" C VAL I 66 " pdb=" CA VAL I 66 " pdb=" CB VAL I 66 " ideal model delta sigma weight residual 110.82 103.89 6.93 1.54e+00 4.22e-01 2.03e+01 ... (remaining 36925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 15241 17.70 - 35.39: 839 35.39 - 53.09: 121 53.09 - 70.78: 48 70.78 - 88.48: 17 Dihedral angle restraints: 16266 sinusoidal: 6469 harmonic: 9797 Sorted by residual: dihedral pdb=" CA MET K 301 " pdb=" C MET K 301 " pdb=" N PHE K 302 " pdb=" CA PHE K 302 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET I 301 " pdb=" C MET I 301 " pdb=" N PHE I 302 " pdb=" CA PHE I 302 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA MET J 301 " pdb=" C MET J 301 " pdb=" N PHE J 302 " pdb=" CA PHE J 302 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 16263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3168 0.043 - 0.085: 974 0.085 - 0.128: 272 0.128 - 0.170: 31 0.170 - 0.213: 6 Chirality restraints: 4451 Sorted by residual: chirality pdb=" CA VAL I 66 " pdb=" N VAL I 66 " pdb=" C VAL I 66 " pdb=" CB VAL I 66 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR J 275 " pdb=" N THR J 275 " pdb=" C THR J 275 " pdb=" CB THR J 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR K 275 " pdb=" N THR K 275 " pdb=" C THR K 275 " pdb=" CB THR K 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4448 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " 0.034 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO J 16 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 15 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO I 16 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 16 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 16 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 202 " 0.016 2.00e-02 2.50e+03 1.38e-02 3.32e+00 pdb=" CG PHE J 202 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE J 202 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 202 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE J 202 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE J 202 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 202 " 0.002 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 8591 2.84 - 3.41: 27984 3.41 - 3.99: 50283 3.99 - 4.56: 72618 4.56 - 5.14: 107422 Nonbonded interactions: 266898 Sorted by model distance: nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU I 383 " pdb=" OG1 THR I 398 " model vdw 2.266 3.040 nonbonded pdb=" O ALA L 55 " pdb=" OG1 THR L 59 " model vdw 2.280 3.040 nonbonded pdb=" O LEU I 34 " pdb=" OG SER I 40 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.287 3.040 ... (remaining 266893 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 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'B' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'C' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'D' and (resid 7 through 184 or resid 204 through 221)) selection = (chain 'E' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'F' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'G' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'H' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 61.650 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.059 27213 Z= 0.227 Angle : 0.599 11.605 36930 Z= 0.341 Chirality : 0.044 0.213 4451 Planarity : 0.004 0.050 4527 Dihedral : 11.901 88.481 9960 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 5.16 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -2.19 (0.12), residues: 3383 helix: -1.81 (0.09), residues: 1827 sheet: 0.23 (0.26), residues: 434 loop : -1.14 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 181 HIS 0.005 0.001 HIS G 185 PHE 0.032 0.001 PHE J 202 TYR 0.010 0.001 TYR H 108 ARG 0.002 0.000 ARG K 111 Details of bonding type rmsd hydrogen bonds : bond 0.26019 ( 1528) hydrogen bonds : angle 8.37910 ( 4413) covalent geometry : bond 0.00445 (27213) covalent geometry : angle 0.59935 (36930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 723 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 SER cc_start: 0.8722 (t) cc_final: 0.8468 (m) REVERT: E 62 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6729 (mt-10) REVERT: E 85 SER cc_start: 0.8527 (t) cc_final: 0.8327 (m) REVERT: F 24 GLU cc_start: 0.7218 (tp30) cc_final: 0.6953 (tp30) REVERT: F 38 ASN cc_start: 0.8485 (t0) cc_final: 0.8128 (t0) REVERT: F 155 GLU cc_start: 0.7136 (tt0) cc_final: 0.6841 (tm-30) REVERT: J 188 TYR cc_start: 0.8752 (m-80) cc_final: 0.8550 (m-80) REVERT: K 158 TRP cc_start: 0.8135 (m100) cc_final: 0.7886 (m-90) REVERT: K 222 LYS cc_start: 0.7542 (pttm) cc_final: 0.7341 (mmmt) REVERT: K 299 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8643 (tp) REVERT: K 402 THR cc_start: 0.8803 (p) cc_final: 0.8543 (p) REVERT: L 24 PHE cc_start: 0.7820 (t80) cc_final: 0.7524 (t80) REVERT: L 127 ILE cc_start: 0.8151 (mm) cc_final: 0.7333 (pt) outliers start: 45 outliers final: 12 residues processed: 758 average time/residue: 1.2523 time to fit residues: 1110.2995 Evaluate side-chains 485 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 472 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 264 optimal weight: 0.0030 chunk 102 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 306 optimal weight: 0.4980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 210 HIS D 8 GLN D 143 ASN D 210 HIS E 134 GLN F 185 HIS G 83 GLN H 81 ASN I 227 HIS K 85 GLN K 155 GLN K 195 ASN K 253 ASN L 282 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127273 restraints weight = 32393.408| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.87 r_work: 0.3267 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27213 Z= 0.138 Angle : 0.551 7.456 36930 Z= 0.293 Chirality : 0.043 0.176 4451 Planarity : 0.004 0.052 4527 Dihedral : 10.143 89.337 3891 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.57 % Allowed : 12.89 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 0.11 (0.13), residues: 3383 helix: 0.69 (0.11), residues: 1892 sheet: -0.09 (0.26), residues: 392 loop : -0.80 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 181 HIS 0.004 0.001 HIS B 185 PHE 0.037 0.001 PHE J 202 TYR 0.019 0.001 TYR B 107 ARG 0.010 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 1528) hydrogen bonds : angle 4.69394 ( 4413) covalent geometry : bond 0.00292 (27213) covalent geometry : angle 0.55079 (36930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 470 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8245 (mmtm) REVERT: B 40 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: C 85 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8169 (m) REVERT: C 188 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6611 (t0) REVERT: E 59 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: F 59 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: F 155 GLU cc_start: 0.7085 (tt0) cc_final: 0.5940 (tm-30) REVERT: F 208 MET cc_start: 0.6359 (ttp) cc_final: 0.5518 (ptm) REVERT: G 134 GLN cc_start: 0.8139 (mp10) cc_final: 0.7591 (mp10) REVERT: G 138 ASP cc_start: 0.8166 (t0) cc_final: 0.7924 (m-30) REVERT: H 151 TYR cc_start: 0.8085 (m-80) cc_final: 0.7688 (m-80) REVERT: I 158 TRP cc_start: 0.8043 (m100) cc_final: 0.7822 (m-90) REVERT: I 170 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7878 (mp) REVERT: I 424 VAL cc_start: 0.8764 (t) cc_final: 0.8527 (m) REVERT: J 71 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7922 (tm-30) REVERT: J 250 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7516 (mt-10) REVERT: K 71 GLN cc_start: 0.8170 (tp40) cc_final: 0.7797 (tm-30) REVERT: K 97 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7611 (mm) REVERT: K 222 LYS cc_start: 0.8192 (pttm) cc_final: 0.7584 (mmmt) REVERT: K 402 THR cc_start: 0.8739 (p) cc_final: 0.8531 (p) REVERT: L 24 PHE cc_start: 0.7699 (t80) cc_final: 0.7183 (t80) REVERT: L 217 LYS cc_start: 0.7871 (ptmt) cc_final: 0.7269 (mmmt) REVERT: L 250 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8108 (mm-30) outliers start: 103 outliers final: 30 residues processed: 540 average time/residue: 1.1994 time to fit residues: 765.4816 Evaluate side-chains 454 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 100 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN D 8 GLN D 134 GLN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127769 restraints weight = 32273.966| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.97 r_work: 0.3269 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27213 Z= 0.125 Angle : 0.514 7.179 36930 Z= 0.270 Chirality : 0.042 0.199 4451 Planarity : 0.004 0.050 4527 Dihedral : 9.302 89.232 3872 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.50 % Allowed : 14.21 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 0.83 (0.14), residues: 3383 helix: 1.51 (0.12), residues: 1905 sheet: -0.18 (0.27), residues: 362 loop : -0.82 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 181 HIS 0.003 0.001 HIS B 185 PHE 0.034 0.001 PHE J 202 TYR 0.013 0.001 TYR A 107 ARG 0.013 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1528) hydrogen bonds : angle 4.31010 ( 4413) covalent geometry : bond 0.00274 (27213) covalent geometry : angle 0.51357 (36930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 430 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7485 (pp20) REVERT: C 85 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8102 (m) REVERT: C 188 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6619 (t0) REVERT: D 131 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8279 (mttp) REVERT: E 31 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7152 (mt-10) REVERT: F 31 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: F 59 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: F 155 GLU cc_start: 0.7051 (tt0) cc_final: 0.6446 (mt-10) REVERT: F 208 MET cc_start: 0.6407 (ttp) cc_final: 0.5503 (ptm) REVERT: G 134 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: H 151 TYR cc_start: 0.8033 (m-80) cc_final: 0.7528 (m-80) REVERT: I 333 LYS cc_start: 0.7854 (mttt) cc_final: 0.7561 (mtpp) REVERT: I 340 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8480 (mtp180) REVERT: I 395 MET cc_start: 0.8445 (mtp) cc_final: 0.8243 (mtp) REVERT: I 424 VAL cc_start: 0.8739 (t) cc_final: 0.8483 (m) REVERT: J 71 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7938 (tm-30) REVERT: J 237 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7730 (tmt) REVERT: J 250 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7737 (mm-30) REVERT: K 222 LYS cc_start: 0.8236 (pttm) cc_final: 0.7593 (mmmt) REVERT: K 299 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (tp) REVERT: K 374 GLN cc_start: 0.8091 (mp10) cc_final: 0.7832 (mp10) REVERT: K 402 THR cc_start: 0.8728 (p) cc_final: 0.8519 (p) REVERT: L 106 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8390 (mm) REVERT: L 217 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7299 (mmmt) outliers start: 101 outliers final: 40 residues processed: 502 average time/residue: 1.2385 time to fit residues: 737.8440 Evaluate side-chains 440 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 191 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 309 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 253 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS B 105 GLN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 210 HIS ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128371 restraints weight = 32601.671| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.97 r_work: 0.3277 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27213 Z= 0.114 Angle : 0.494 7.005 36930 Z= 0.259 Chirality : 0.042 0.179 4451 Planarity : 0.003 0.059 4527 Dihedral : 8.987 86.901 3872 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.53 % Allowed : 14.66 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.13 (0.14), residues: 3383 helix: 1.86 (0.12), residues: 1897 sheet: -0.42 (0.26), residues: 356 loop : -0.76 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 181 HIS 0.003 0.001 HIS B 185 PHE 0.033 0.001 PHE J 202 TYR 0.018 0.001 TYR B 151 ARG 0.011 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 1528) hydrogen bonds : angle 4.12956 ( 4413) covalent geometry : bond 0.00250 (27213) covalent geometry : angle 0.49388 (36930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 407 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.8863 (t) cc_final: 0.8578 (m) REVERT: B 40 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7495 (pp20) REVERT: C 85 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8036 (m) REVERT: C 188 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6653 (t0) REVERT: D 131 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8258 (mttp) REVERT: E 31 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7118 (mt-10) REVERT: E 59 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 86 THR cc_start: 0.8580 (t) cc_final: 0.8298 (m) REVERT: E 95 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7257 (mt) REVERT: F 31 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: F 59 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: F 145 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6639 (pt) REVERT: F 155 GLU cc_start: 0.6953 (tt0) cc_final: 0.6267 (mt-10) REVERT: F 184 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5928 (ptmm) REVERT: F 208 MET cc_start: 0.6337 (ttp) cc_final: 0.5492 (ptm) REVERT: H 151 TYR cc_start: 0.7959 (m-80) cc_final: 0.7534 (m-80) REVERT: I 74 VAL cc_start: 0.8000 (t) cc_final: 0.7673 (p) REVERT: I 333 LYS cc_start: 0.7870 (mttt) cc_final: 0.7544 (mtpp) REVERT: I 424 VAL cc_start: 0.8759 (t) cc_final: 0.8509 (m) REVERT: J 71 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8010 (tm-30) REVERT: J 186 MET cc_start: 0.8422 (mtp) cc_final: 0.8093 (mtt) REVERT: J 237 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7771 (tmt) REVERT: J 250 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7632 (mm-30) REVERT: K 97 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7647 (mm) REVERT: K 222 LYS cc_start: 0.8281 (pttm) cc_final: 0.7645 (mmmt) REVERT: K 299 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8742 (tp) REVERT: K 374 GLN cc_start: 0.8137 (mp10) cc_final: 0.7896 (mp10) REVERT: K 402 THR cc_start: 0.8685 (p) cc_final: 0.8430 (p) REVERT: L 181 TRP cc_start: 0.8431 (m-90) cc_final: 0.8211 (m-90) outliers start: 102 outliers final: 43 residues processed: 475 average time/residue: 1.2482 time to fit residues: 702.8861 Evaluate side-chains 443 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 388 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 181 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 167 optimal weight: 0.0670 chunk 172 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127817 restraints weight = 32546.262| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.98 r_work: 0.3256 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27213 Z= 0.124 Angle : 0.503 7.108 36930 Z= 0.263 Chirality : 0.042 0.185 4451 Planarity : 0.003 0.062 4527 Dihedral : 8.868 89.090 3872 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.40 % Allowed : 15.70 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.18 (0.14), residues: 3383 helix: 1.93 (0.12), residues: 1905 sheet: -0.40 (0.26), residues: 362 loop : -0.81 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 181 HIS 0.004 0.001 HIS K 168 PHE 0.033 0.001 PHE J 202 TYR 0.017 0.001 TYR B 151 ARG 0.014 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1528) hydrogen bonds : angle 4.09699 ( 4413) covalent geometry : bond 0.00282 (27213) covalent geometry : angle 0.50255 (36930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 395 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.8864 (t) cc_final: 0.8525 (m) REVERT: A 134 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: B 40 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: C 85 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8055 (m) REVERT: C 188 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6579 (t0) REVERT: D 131 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8278 (mttp) REVERT: E 31 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7245 (mt-10) REVERT: E 59 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: E 86 THR cc_start: 0.8549 (t) cc_final: 0.8224 (m) REVERT: E 95 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7373 (mt) REVERT: F 31 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: F 59 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8300 (mm-30) REVERT: F 155 GLU cc_start: 0.7233 (tt0) cc_final: 0.6552 (mt-10) REVERT: F 184 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5968 (ptmm) REVERT: F 208 MET cc_start: 0.6578 (ttp) cc_final: 0.5776 (ptm) REVERT: H 151 TYR cc_start: 0.7990 (m-80) cc_final: 0.7591 (m-80) REVERT: I 74 VAL cc_start: 0.8047 (t) cc_final: 0.7734 (p) REVERT: I 333 LYS cc_start: 0.7886 (mttt) cc_final: 0.7558 (mtpp) REVERT: I 418 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8706 (tp) REVERT: I 424 VAL cc_start: 0.8844 (t) cc_final: 0.8605 (m) REVERT: I 436 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8208 (mtm110) REVERT: J 71 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8051 (tm-30) REVERT: J 186 MET cc_start: 0.8496 (mtp) cc_final: 0.8282 (mtm) REVERT: J 237 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7925 (tmt) REVERT: J 250 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7689 (mm-30) REVERT: K 97 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7737 (mm) REVERT: K 222 LYS cc_start: 0.8246 (pttm) cc_final: 0.7693 (mmmt) REVERT: K 299 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8722 (tp) REVERT: K 402 THR cc_start: 0.8736 (p) cc_final: 0.8498 (p) REVERT: L 181 TRP cc_start: 0.8434 (m-90) cc_final: 0.8222 (m-90) REVERT: L 217 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7380 (mmmt) REVERT: L 250 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7732 (mt-10) outliers start: 98 outliers final: 54 residues processed: 459 average time/residue: 1.2587 time to fit residues: 689.6917 Evaluate side-chains 447 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 380 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 208 MET Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 231 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 201 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 323 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 319 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 8 GLN D 8 GLN G 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128124 restraints weight = 32331.633| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.04 r_work: 0.3242 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27213 Z= 0.117 Angle : 0.499 7.896 36930 Z= 0.261 Chirality : 0.042 0.193 4451 Planarity : 0.003 0.070 4527 Dihedral : 8.706 87.647 3870 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.57 % Allowed : 16.01 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.21 (0.14), residues: 3383 helix: 2.02 (0.12), residues: 1889 sheet: -0.55 (0.26), residues: 356 loop : -0.83 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 181 HIS 0.004 0.001 HIS K 168 PHE 0.032 0.001 PHE J 202 TYR 0.019 0.001 TYR B 151 ARG 0.015 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1528) hydrogen bonds : angle 4.06244 ( 4413) covalent geometry : bond 0.00265 (27213) covalent geometry : angle 0.49925 (36930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 389 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.8822 (t) cc_final: 0.8479 (m) REVERT: B 40 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: C 85 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.7994 (m) REVERT: C 188 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6561 (t0) REVERT: D 131 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8201 (mttp) REVERT: E 86 THR cc_start: 0.8482 (t) cc_final: 0.8133 (m) REVERT: E 95 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7406 (mt) REVERT: F 31 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: F 59 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: F 145 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6755 (mm) REVERT: F 155 GLU cc_start: 0.7054 (tt0) cc_final: 0.6394 (mt-10) REVERT: F 184 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5944 (ptmm) REVERT: F 208 MET cc_start: 0.6438 (ttp) cc_final: 0.5769 (ptm) REVERT: H 151 TYR cc_start: 0.7916 (m-80) cc_final: 0.7548 (m-80) REVERT: H 211 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8509 (mttt) REVERT: I 74 VAL cc_start: 0.8029 (t) cc_final: 0.7715 (p) REVERT: I 333 LYS cc_start: 0.7686 (mttt) cc_final: 0.7419 (mtpp) REVERT: I 436 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.8038 (mtm110) REVERT: J 71 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7973 (tm-30) REVERT: J 186 MET cc_start: 0.8279 (mtp) cc_final: 0.8049 (mtm) REVERT: J 237 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7691 (tmt) REVERT: J 250 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7513 (mt-10) REVERT: K 97 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7688 (mm) REVERT: K 222 LYS cc_start: 0.8158 (pttm) cc_final: 0.7600 (mmmt) REVERT: K 299 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8688 (tp) REVERT: L 181 TRP cc_start: 0.8381 (m-90) cc_final: 0.8178 (m-90) REVERT: L 217 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7346 (mmmt) REVERT: L 250 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7552 (mt-10) outliers start: 103 outliers final: 57 residues processed: 461 average time/residue: 1.2004 time to fit residues: 654.2211 Evaluate side-chains 440 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 371 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 208 MET Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 209 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 281 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 134 GLN B 105 GLN C 8 GLN D 8 GLN F 134 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124051 restraints weight = 32481.480| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.94 r_work: 0.3211 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27213 Z= 0.205 Angle : 0.571 8.943 36930 Z= 0.298 Chirality : 0.045 0.196 4451 Planarity : 0.004 0.069 4527 Dihedral : 9.020 86.816 3870 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.60 % Allowed : 16.42 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.00 (0.14), residues: 3383 helix: 1.77 (0.12), residues: 1903 sheet: -0.44 (0.25), residues: 398 loop : -0.85 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 181 HIS 0.004 0.001 HIS I 168 PHE 0.035 0.002 PHE J 202 TYR 0.014 0.001 TYR B 107 ARG 0.015 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1528) hydrogen bonds : angle 4.22820 ( 4413) covalent geometry : bond 0.00496 (27213) covalent geometry : angle 0.57113 (36930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 390 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7355 (tt0) cc_final: 0.7115 (tt0) REVERT: B 40 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: C 22 CYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 85 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8417 (m) REVERT: C 188 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6604 (t0) REVERT: D 131 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8372 (mttp) REVERT: E 86 THR cc_start: 0.8662 (t) cc_final: 0.8206 (m) REVERT: E 95 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7492 (mt) REVERT: F 31 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: F 59 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: F 145 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6816 (mm) REVERT: F 155 GLU cc_start: 0.7160 (tt0) cc_final: 0.6540 (mt-10) REVERT: F 184 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5986 (ptmm) REVERT: F 208 MET cc_start: 0.6634 (ttp) cc_final: 0.5735 (ptm) REVERT: G 149 ASP cc_start: 0.7831 (m-30) cc_final: 0.7616 (t0) REVERT: H 8 GLN cc_start: 0.8786 (mt0) cc_final: 0.8533 (mt0) REVERT: H 151 TYR cc_start: 0.8045 (m-80) cc_final: 0.7590 (m-80) REVERT: H 211 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8526 (mttt) REVERT: I 74 VAL cc_start: 0.8051 (t) cc_final: 0.7735 (p) REVERT: I 333 LYS cc_start: 0.7958 (mttt) cc_final: 0.7629 (mtpp) REVERT: I 418 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8749 (tp) REVERT: J 71 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8055 (tm-30) REVERT: J 186 MET cc_start: 0.8528 (mtp) cc_final: 0.8190 (mtt) REVERT: J 237 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7933 (tmt) REVERT: J 250 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7801 (mt-10) REVERT: K 97 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7688 (mm) REVERT: K 142 LEU cc_start: 0.7067 (mm) cc_final: 0.6643 (mp) REVERT: K 222 LYS cc_start: 0.8303 (pttm) cc_final: 0.7659 (mmmt) REVERT: K 299 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8739 (tp) REVERT: L 217 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7418 (mmmt) REVERT: L 250 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7708 (mt-10) REVERT: L 334 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7837 (mmpt) REVERT: L 373 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7268 (mp0) outliers start: 104 outliers final: 54 residues processed: 466 average time/residue: 1.1947 time to fit residues: 659.8458 Evaluate side-chains 451 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 383 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 160 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 299 optimal weight: 0.0970 chunk 293 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 134 GLN B 8 GLN C 8 GLN E 83 GLN E 134 GLN G 134 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127364 restraints weight = 32391.446| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.98 r_work: 0.3234 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27213 Z= 0.123 Angle : 0.523 9.079 36930 Z= 0.273 Chirality : 0.042 0.178 4451 Planarity : 0.004 0.064 4527 Dihedral : 8.773 88.185 3870 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.08 % Allowed : 17.78 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.19 (0.14), residues: 3383 helix: 2.01 (0.12), residues: 1875 sheet: -0.46 (0.25), residues: 398 loop : -0.84 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 181 HIS 0.004 0.001 HIS K 168 PHE 0.032 0.001 PHE J 202 TYR 0.013 0.001 TYR A 107 ARG 0.014 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1528) hydrogen bonds : angle 4.10148 ( 4413) covalent geometry : bond 0.00278 (27213) covalent geometry : angle 0.52282 (36930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 377 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7476 (tt0) cc_final: 0.7236 (tt0) REVERT: B 40 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: C 85 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8350 (m) REVERT: C 188 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6576 (t0) REVERT: D 131 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8325 (mttp) REVERT: E 86 THR cc_start: 0.8523 (t) cc_final: 0.8152 (m) REVERT: E 95 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7435 (mt) REVERT: F 31 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: F 59 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: F 145 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6901 (pt) REVERT: F 155 GLU cc_start: 0.7299 (tt0) cc_final: 0.6603 (mt-10) REVERT: F 184 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5915 (ptmm) REVERT: F 208 MET cc_start: 0.6630 (ttp) cc_final: 0.5946 (ptm) REVERT: G 190 CYS cc_start: 0.7769 (t) cc_final: 0.7304 (p) REVERT: H 8 GLN cc_start: 0.8714 (mt0) cc_final: 0.8492 (mt0) REVERT: H 151 TYR cc_start: 0.8009 (m-80) cc_final: 0.7573 (m-80) REVERT: H 211 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8511 (mttt) REVERT: I 74 VAL cc_start: 0.8164 (t) cc_final: 0.7846 (p) REVERT: I 91 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5758 (t80) REVERT: I 333 LYS cc_start: 0.7852 (mttt) cc_final: 0.7621 (mtpp) REVERT: I 418 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8788 (tp) REVERT: J 71 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8152 (tm-30) REVERT: J 237 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8016 (tmt) REVERT: J 250 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7771 (mt-10) REVERT: K 97 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7746 (mm) REVERT: K 142 LEU cc_start: 0.7134 (mm) cc_final: 0.6714 (mp) REVERT: K 222 LYS cc_start: 0.8270 (pttm) cc_final: 0.7680 (mmmt) REVERT: K 299 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8716 (tp) REVERT: L 217 LYS cc_start: 0.7977 (ptmt) cc_final: 0.7502 (mmmt) REVERT: L 250 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7736 (mt-10) REVERT: L 334 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7820 (mmpt) outliers start: 89 outliers final: 46 residues processed: 445 average time/residue: 1.2376 time to fit residues: 650.2563 Evaluate side-chains 420 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 360 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 72 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 134 GLN B 8 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN E 83 GLN E 134 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127405 restraints weight = 32518.172| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.07 r_work: 0.3247 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27213 Z= 0.132 Angle : 0.532 9.378 36930 Z= 0.278 Chirality : 0.043 0.182 4451 Planarity : 0.004 0.079 4527 Dihedral : 8.686 89.195 3870 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.56 % Allowed : 18.61 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.19 (0.14), residues: 3383 helix: 2.01 (0.12), residues: 1875 sheet: -0.56 (0.25), residues: 392 loop : -0.80 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 181 HIS 0.005 0.001 HIS A 210 PHE 0.038 0.001 PHE G 217 TYR 0.018 0.001 TYR G 151 ARG 0.018 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1528) hydrogen bonds : angle 4.09571 ( 4413) covalent geometry : bond 0.00306 (27213) covalent geometry : angle 0.53169 (36930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: C 85 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8304 (m) REVERT: C 188 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6642 (t0) REVERT: D 131 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8316 (mttp) REVERT: E 86 THR cc_start: 0.8568 (t) cc_final: 0.8182 (m) REVERT: E 95 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7384 (mt) REVERT: F 31 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: F 59 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: F 145 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6773 (pt) REVERT: F 155 GLU cc_start: 0.7199 (tt0) cc_final: 0.6574 (mt-10) REVERT: F 208 MET cc_start: 0.6566 (ttp) cc_final: 0.5759 (ptm) REVERT: G 190 CYS cc_start: 0.7662 (t) cc_final: 0.7280 (p) REVERT: H 8 GLN cc_start: 0.8698 (mt0) cc_final: 0.8470 (mt0) REVERT: H 151 TYR cc_start: 0.7984 (m-80) cc_final: 0.7550 (m-80) REVERT: H 184 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7996 (mtpt) REVERT: H 211 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8548 (mttp) REVERT: I 74 VAL cc_start: 0.8104 (t) cc_final: 0.7811 (p) REVERT: I 333 LYS cc_start: 0.7847 (mttt) cc_final: 0.7535 (mtpp) REVERT: I 418 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8753 (tp) REVERT: J 71 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8086 (tm-30) REVERT: J 186 MET cc_start: 0.8519 (mtp) cc_final: 0.8203 (mtt) REVERT: J 237 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7885 (tmt) REVERT: J 250 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7767 (mt-10) REVERT: K 142 LEU cc_start: 0.7094 (mm) cc_final: 0.6660 (mp) REVERT: K 222 LYS cc_start: 0.8314 (pttm) cc_final: 0.7668 (mmmt) REVERT: K 299 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8735 (tp) REVERT: L 217 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7408 (mmmt) REVERT: L 250 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7660 (mt-10) REVERT: L 334 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7800 (mmpt) outliers start: 74 outliers final: 47 residues processed: 426 average time/residue: 1.3173 time to fit residues: 661.6096 Evaluate side-chains 418 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 359 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 97 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 305 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 134 GLN B 105 GLN E 83 GLN G 134 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.161294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125015 restraints weight = 32421.552| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.92 r_work: 0.3226 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27213 Z= 0.189 Angle : 0.576 9.911 36930 Z= 0.300 Chirality : 0.044 0.191 4451 Planarity : 0.004 0.077 4527 Dihedral : 8.912 88.740 3870 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.43 % Allowed : 18.85 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.06 (0.14), residues: 3383 helix: 1.82 (0.12), residues: 1895 sheet: -0.56 (0.25), residues: 392 loop : -0.77 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 181 HIS 0.008 0.001 HIS L 168 PHE 0.034 0.002 PHE J 202 TYR 0.017 0.001 TYR G 151 ARG 0.017 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1528) hydrogen bonds : angle 4.22749 ( 4413) covalent geometry : bond 0.00459 (27213) covalent geometry : angle 0.57597 (36930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 374 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: C 22 CYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8607 (m) REVERT: C 85 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8427 (m) REVERT: C 188 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6637 (t0) REVERT: D 131 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8385 (mttp) REVERT: E 86 THR cc_start: 0.8628 (t) cc_final: 0.8159 (m) REVERT: E 95 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7486 (mt) REVERT: F 31 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: F 59 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: F 145 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6783 (pt) REVERT: F 155 GLU cc_start: 0.7251 (tt0) cc_final: 0.6562 (mt-10) REVERT: F 184 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5904 (tptp) REVERT: F 208 MET cc_start: 0.6584 (ttp) cc_final: 0.5751 (ptm) REVERT: G 190 CYS cc_start: 0.7636 (t) cc_final: 0.7209 (p) REVERT: H 8 GLN cc_start: 0.8782 (mt0) cc_final: 0.8545 (mt0) REVERT: H 151 TYR cc_start: 0.8049 (m-80) cc_final: 0.7569 (m-80) REVERT: H 184 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: I 74 VAL cc_start: 0.8108 (t) cc_final: 0.7799 (p) REVERT: I 333 LYS cc_start: 0.7969 (mttt) cc_final: 0.7647 (mtpp) REVERT: I 418 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8741 (tp) REVERT: J 71 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8121 (tm-30) REVERT: J 186 MET cc_start: 0.8566 (mtp) cc_final: 0.8280 (mtm) REVERT: J 250 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7795 (mt-10) REVERT: K 142 LEU cc_start: 0.7112 (mm) cc_final: 0.6671 (mp) REVERT: K 222 LYS cc_start: 0.8277 (pttm) cc_final: 0.7644 (mmmt) REVERT: K 299 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8721 (tp) REVERT: L 217 LYS cc_start: 0.7956 (ptmt) cc_final: 0.7448 (mmmt) REVERT: L 250 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7699 (mt-10) REVERT: L 334 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7836 (mmpt) REVERT: L 373 GLU cc_start: 0.7659 (mp0) cc_final: 0.7307 (mp0) outliers start: 70 outliers final: 44 residues processed: 426 average time/residue: 1.3763 time to fit residues: 698.7569 Evaluate side-chains 414 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 288 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 308 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 299 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 295 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN E 134 GLN K 71 GLN L 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128954 restraints weight = 32447.638| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3277 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27213 Z= 0.112 Angle : 0.522 10.195 36930 Z= 0.272 Chirality : 0.042 0.178 4451 Planarity : 0.004 0.080 4527 Dihedral : 8.495 87.758 3870 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.18 % Allowed : 19.30 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.29 (0.15), residues: 3383 helix: 2.08 (0.12), residues: 1887 sheet: -0.50 (0.25), residues: 392 loop : -0.76 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 181 HIS 0.007 0.001 HIS K 168 PHE 0.033 0.001 PHE J 202 TYR 0.020 0.001 TYR E 144 ARG 0.018 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 1528) hydrogen bonds : angle 4.05769 ( 4413) covalent geometry : bond 0.00251 (27213) covalent geometry : angle 0.52173 (36930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24992.42 seconds wall clock time: 436 minutes 10.86 seconds (26170.86 seconds total)