Starting phenix.real_space_refine on Fri Jan 17 12:18:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517.map" model { file = "/net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt3_43517/01_2025/8vt3_43517_neut.cif" } resolution = 3.33 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= 0.001 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6732 2.51 5 N 1818 2.21 5 O 2145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10758 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "H" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "I" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.04, per 1000 atoms: 0.65 Number of scatterers: 10758 At special positions: 0 Unit cell: (89.18, 88.27, 141.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2145 8.00 N 1818 7.00 C 6732 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 1 " - " ASN G 172 " " NAG E 1 " - " ASN A 57 " " NAG F 1 " - " ASN H 172 " " NAG J 1 " - " ASN B 57 " " NAG K 1 " - " ASN I 172 " " NAG L 1 " - " ASN C 57 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 33.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.901A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.902A pdb=" N ASN C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 58' Processing helix chain 'C' and resid 65 through 82 removed outlier: 3.882A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 109 removed outlier: 3.819A pdb=" N ALA G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.547A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 138 removed outlier: 3.672A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 172 removed outlier: 3.663A pdb=" N PHE G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 197 removed outlier: 4.098A pdb=" N SER G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN G 197 " --> pdb=" O PHE G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 210 removed outlier: 3.697A pdb=" N ARG G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 206 " --> pdb=" O ASN G 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 209 " --> pdb=" O ARG G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 234 removed outlier: 3.524A pdb=" N MET G 234 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 246 removed outlier: 3.719A pdb=" N LEU G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 255 removed outlier: 4.171A pdb=" N ARG G 252 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG G 253 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS G 254 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY G 255 " --> pdb=" O ARG G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.981A pdb=" N LYS G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 350 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN G 351 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 446 removed outlier: 3.572A pdb=" N PHE G 446 " --> pdb=" O SER G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 486 removed outlier: 3.769A pdb=" N PHE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 470 " --> pdb=" O ASN G 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 480 " --> pdb=" O LYS G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 481 " --> pdb=" O PHE G 477 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU G 485 " --> pdb=" O LEU G 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 109 removed outlier: 3.833A pdb=" N ALA H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.581A pdb=" N ALA H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 removed outlier: 3.724A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 172 removed outlier: 3.818A pdb=" N ASP H 167 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 176 Processing helix chain 'H' and resid 188 through 197 removed outlier: 4.172A pdb=" N SER H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 197 " --> pdb=" O PHE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 210 removed outlier: 3.558A pdb=" N ARG H 205 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN H 206 " --> pdb=" O ASN H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.725A pdb=" N ALA H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 234 No H-bonds generated for 'chain 'H' and resid 232 through 234' Processing helix chain 'H' and resid 237 through 247 removed outlier: 3.616A pdb=" N ILE H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 255 removed outlier: 4.233A pdb=" N ARG H 252 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG H 253 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 255 " --> pdb=" O ARG H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 344 through 352 removed outlier: 3.939A pdb=" N LYS H 348 " --> pdb=" O GLU H 345 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 351 " --> pdb=" O LYS H 348 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 352 " --> pdb=" O GLU H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 446 removed outlier: 3.585A pdb=" N PHE H 446 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 486 removed outlier: 3.652A pdb=" N PHE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP H 473 " --> pdb=" O ASN H 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 474 " --> pdb=" O SER H 470 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 482 " --> pdb=" O ASP H 478 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 109 removed outlier: 3.528A pdb=" N ILE I 108 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 109' Processing helix chain 'I' and resid 111 through 129 removed outlier: 3.515A pdb=" N ALA I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 128 " --> pdb=" O ILE I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.664A pdb=" N THR I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA I 136 " --> pdb=" O SER I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 removed outlier: 3.648A pdb=" N ASP I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU I 173 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 removed outlier: 4.061A pdb=" N ASN I 197 " --> pdb=" O PHE I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 207 removed outlier: 3.891A pdb=" N ARG I 205 " --> pdb=" O LEU I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 234 removed outlier: 3.619A pdb=" N MET I 234 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 246 removed outlier: 3.682A pdb=" N LEU I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU I 246 " --> pdb=" O LYS I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 255 removed outlier: 4.200A pdb=" N ARG I 252 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG I 253 " --> pdb=" O MET I 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS I 254 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY I 255 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 344 through 349 removed outlier: 3.948A pdb=" N LYS I 348 " --> pdb=" O GLU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 445 Processing helix chain 'I' and resid 460 through 486 removed outlier: 3.796A pdb=" N PHE I 464 " --> pdb=" O LEU I 460 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU I 465 " --> pdb=" O ASP I 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE I 467 " --> pdb=" O VAL I 463 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER I 470 " --> pdb=" O ASN I 466 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL I 474 " --> pdb=" O SER I 470 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU I 479 " --> pdb=" O ARG I 475 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU I 481 " --> pdb=" O PHE I 477 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 482 " --> pdb=" O ASP I 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU I 485 " --> pdb=" O LEU I 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 328 through 329 removed outlier: 3.659A pdb=" N HIS G 332 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL G 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 36 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER A 29 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA G 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 31 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A 33 " --> pdb=" O TRP G 284 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TRP G 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR A 35 " --> pdb=" O PRO G 282 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER A 37 " --> pdb=" O ASP G 280 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL G 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP G 309 " --> pdb=" O TYR G 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 328 through 329 removed outlier: 3.659A pdb=" N HIS G 332 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL G 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 36 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 21 " --> pdb=" O HIS G 435 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE G 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR A 23 " --> pdb=" O ILE G 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.330A pdb=" N THR A 45 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR G 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET G 270 " --> pdb=" O LEU G 259 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU G 259 " --> pdb=" O MET G 270 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN G 272 " --> pdb=" O GLY G 257 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY G 257 " --> pdb=" O GLN G 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 328 through 329 removed outlier: 3.668A pdb=" N HIS H 332 " --> pdb=" O ARG H 329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 40 " --> pdb=" O CYS H 335 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER B 29 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA H 288 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE B 31 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL H 286 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU B 33 " --> pdb=" O TRP H 284 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TRP H 284 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 35 " --> pdb=" O PRO H 282 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B 37 " --> pdb=" O ASP H 280 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL H 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY H 308 " --> pdb=" O VAL H 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 328 through 329 removed outlier: 3.668A pdb=" N HIS H 332 " --> pdb=" O ARG H 329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 40 " --> pdb=" O CYS H 335 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 21 " --> pdb=" O HIS H 435 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE H 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 23 " --> pdb=" O ILE H 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 146 through 150 removed outlier: 8.526A pdb=" N ARG H 156 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR B 45 " --> pdb=" O ARG H 156 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL H 262 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE H 268 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 256 " --> pdb=" O GLN H 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 318 through 320 removed outlier: 3.633A pdb=" N TRP I 309 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER C 37 " --> pdb=" O ASP I 280 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 35 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP I 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU C 33 " --> pdb=" O TRP I 284 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE C 31 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA I 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 29 " --> pdb=" O ALA I 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS I 332 " --> pdb=" O ARG I 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 318 through 320 removed outlier: 3.633A pdb=" N TRP I 309 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER C 37 " --> pdb=" O ASP I 280 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 35 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP I 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU C 33 " --> pdb=" O TRP I 284 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE C 31 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA I 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 29 " --> pdb=" O ALA I 288 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU C 21 " --> pdb=" O HIS I 435 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE I 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR C 23 " --> pdb=" O ILE I 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.287A pdb=" N THR C 45 " --> pdb=" O ARG I 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR I 269 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET I 270 " --> pdb=" O LEU I 259 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 259 " --> pdb=" O MET I 270 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN I 272 " --> pdb=" O GLY I 257 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLY I 257 " --> pdb=" O GLN I 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'G' and resid 362 through 363 Processing sheet with id=AB3, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AB4, first strand: chain 'G' and resid 398 through 402 removed outlier: 7.181A pdb=" N ILE G 392 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN G 402 " --> pdb=" O CYS G 390 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N CYS G 390 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 294 through 295 Processing sheet with id=AB6, first strand: chain 'H' and resid 303 through 304 Processing sheet with id=AB7, first strand: chain 'H' and resid 372 through 376 Processing sheet with id=AB8, first strand: chain 'H' and resid 399 through 401 removed outlier: 7.195A pdb=" N ILE H 392 " --> pdb=" O ILE H 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 294 through 295 removed outlier: 3.705A pdb=" N ASN I 298 " --> pdb=" O LYS I 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 303 through 304 Processing sheet with id=AC2, first strand: chain 'I' and resid 372 through 376 removed outlier: 3.545A pdb=" N GLY I 379 " --> pdb=" O SER I 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS I 384 " --> pdb=" O GLY I 406 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 399 through 402 removed outlier: 7.006A pdb=" N ILE I 392 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN I 402 " --> pdb=" O CYS I 390 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N CYS I 390 " --> pdb=" O GLN I 402 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 417 " --> pdb=" O GLY I 393 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3237 1.33 - 1.45: 1420 1.45 - 1.57: 6167 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10908 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.73e+00 ... (remaining 10903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 14169 1.94 - 3.88: 526 3.88 - 5.82: 61 5.82 - 7.76: 16 7.76 - 9.70: 3 Bond angle restraints: 14775 Sorted by residual: angle pdb=" N THR H 174 " pdb=" CA THR H 174 " pdb=" C THR H 174 " ideal model delta sigma weight residual 113.20 108.56 4.64 1.36e+00 5.41e-01 1.17e+01 angle pdb=" C THR H 411 " pdb=" N ASN H 412 " pdb=" CA ASN H 412 " ideal model delta sigma weight residual 121.94 115.38 6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" N ILE G 124 " pdb=" CA ILE G 124 " pdb=" C ILE G 124 " ideal model delta sigma weight residual 113.42 109.80 3.62 1.17e+00 7.31e-01 9.56e+00 angle pdb=" C ILE I 420 " pdb=" N ASP I 421 " pdb=" CA ASP I 421 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.76e+00 angle pdb=" CA LEU C 50 " pdb=" CB LEU C 50 " pdb=" CG LEU C 50 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6437 23.98 - 47.96: 313 47.96 - 71.94: 55 71.94 - 95.92: 40 95.92 - 119.90: 31 Dihedral angle restraints: 6876 sinusoidal: 2892 harmonic: 3984 Sorted by residual: dihedral pdb=" CA TYR G 385 " pdb=" C TYR G 385 " pdb=" N LYS G 386 " pdb=" CA LYS G 386 " ideal model delta harmonic sigma weight residual 180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR I 385 " pdb=" C TYR I 385 " pdb=" N LYS I 386 " pdb=" CA LYS I 386 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR H 385 " pdb=" C TYR H 385 " pdb=" N LYS H 386 " pdb=" CA LYS H 386 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1246 0.059 - 0.117: 481 0.117 - 0.176: 65 0.176 - 0.235: 1 0.235 - 0.294: 4 Chirality restraints: 1797 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN G 172 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1794 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 193 " 0.017 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE I 193 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE I 193 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE I 193 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 193 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 193 " 0.018 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE G 193 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE G 193 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 193 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 193 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 193 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 193 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR G 359 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO G 360 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 360 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 360 " -0.028 5.00e-02 4.00e+02 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 409 2.70 - 3.25: 9815 3.25 - 3.80: 14320 3.80 - 4.35: 18965 4.35 - 4.90: 34740 Nonbonded interactions: 78249 Sorted by model distance: nonbonded pdb=" OD1 ASN H 353 " pdb=" OG1 THR H 356 " model vdw 2.153 3.040 nonbonded pdb=" O LEU H 141 " pdb=" NH2 ARG H 163 " model vdw 2.176 3.120 nonbonded pdb=" ND2 ASN I 353 " pdb=" OG1 THR I 356 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN H 272 " model vdw 2.219 3.040 nonbonded pdb=" ND2 ASN I 412 " pdb=" O SER I 428 " model vdw 2.297 3.120 ... (remaining 78244 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.860 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.084 10908 Z= 0.743 Angle : 0.872 9.698 14775 Z= 0.458 Chirality : 0.058 0.294 1797 Planarity : 0.005 0.052 1872 Dihedral : 18.193 119.897 4302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.20), residues: 1365 helix: -2.93 (0.22), residues: 369 sheet: -1.51 (0.28), residues: 318 loop : -2.44 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 284 HIS 0.005 0.002 HIS I 332 PHE 0.047 0.003 PHE I 193 TYR 0.020 0.004 TYR I 310 ARG 0.016 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.211 Fit side-chains REVERT: A 54 ASP cc_start: 0.7255 (p0) cc_final: 0.6722 (p0) REVERT: H 325 ASP cc_start: 0.7314 (m-30) cc_final: 0.7006 (m-30) REVERT: H 353 ASN cc_start: 0.7862 (t0) cc_final: 0.7602 (t0) REVERT: I 325 ASP cc_start: 0.7698 (m-30) cc_final: 0.7452 (m-30) REVERT: I 471 GLN cc_start: 0.8105 (tp40) cc_final: 0.7414 (tm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2542 time to fit residues: 40.7045 Evaluate side-chains 90 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118566 restraints weight = 12731.797| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.06 r_work: 0.3199 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10908 Z= 0.197 Angle : 0.646 11.182 14775 Z= 0.323 Chirality : 0.047 0.212 1797 Planarity : 0.005 0.043 1872 Dihedral : 14.090 95.365 1845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.34 % Allowed : 6.07 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1365 helix: -1.94 (0.24), residues: 414 sheet: -1.06 (0.33), residues: 258 loop : -1.98 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 284 HIS 0.002 0.001 HIS I 332 PHE 0.014 0.001 PHE G 193 TYR 0.017 0.001 TYR I 385 ARG 0.006 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.229 Fit side-chains REVERT: A 54 ASP cc_start: 0.7682 (p0) cc_final: 0.7129 (p0) REVERT: G 478 ASP cc_start: 0.7773 (t0) cc_final: 0.7522 (t0) REVERT: H 325 ASP cc_start: 0.7785 (m-30) cc_final: 0.7437 (m-30) REVERT: H 353 ASN cc_start: 0.8361 (t0) cc_final: 0.8054 (t0) REVERT: I 471 GLN cc_start: 0.7754 (tp40) cc_final: 0.7188 (tm-30) outliers start: 4 outliers final: 3 residues processed: 104 average time/residue: 0.2341 time to fit residues: 35.4811 Evaluate side-chains 93 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 90 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.083732 restraints weight = 13252.619| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.87 r_work: 0.2637 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10908 Z= 0.178 Angle : 0.549 7.272 14775 Z= 0.278 Chirality : 0.044 0.246 1797 Planarity : 0.004 0.042 1872 Dihedral : 8.535 78.844 1845 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.68 % Allowed : 7.86 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.22), residues: 1365 helix: -1.36 (0.26), residues: 414 sheet: -0.71 (0.33), residues: 258 loop : -1.81 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.001 0.000 HIS H 435 PHE 0.014 0.001 PHE G 193 TYR 0.012 0.001 TYR I 385 ARG 0.006 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.289 Fit side-chains REVERT: G 477 PHE cc_start: 0.7719 (t80) cc_final: 0.7516 (t80) REVERT: G 478 ASP cc_start: 0.7836 (t0) cc_final: 0.7493 (t0) REVERT: H 325 ASP cc_start: 0.7559 (m-30) cc_final: 0.7350 (m-30) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.2408 time to fit residues: 36.0743 Evaluate side-chains 92 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain H residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 116 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.111384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.085836 restraints weight = 13081.524| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.84 r_work: 0.2668 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10908 Z= 0.129 Angle : 0.501 7.763 14775 Z= 0.259 Chirality : 0.043 0.261 1797 Planarity : 0.003 0.041 1872 Dihedral : 7.212 70.110 1845 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.68 % Allowed : 9.32 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1365 helix: -1.00 (0.27), residues: 411 sheet: -0.44 (0.33), residues: 258 loop : -1.68 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.008 0.001 PHE G 193 TYR 0.013 0.001 TYR H 385 ARG 0.005 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.244 Fit side-chains REVERT: G 478 ASP cc_start: 0.7808 (t0) cc_final: 0.7482 (t0) REVERT: H 353 ASN cc_start: 0.8316 (t0) cc_final: 0.8023 (t0) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.2528 time to fit residues: 36.7470 Evaluate side-chains 94 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120563 restraints weight = 12667.613| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.25 r_work: 0.3206 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10908 Z= 0.214 Angle : 0.532 8.773 14775 Z= 0.272 Chirality : 0.044 0.262 1797 Planarity : 0.004 0.043 1872 Dihedral : 6.649 63.178 1845 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.23), residues: 1365 helix: -0.99 (0.26), residues: 414 sheet: -0.39 (0.33), residues: 258 loop : -1.68 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 284 HIS 0.001 0.000 HIS I 332 PHE 0.011 0.001 PHE G 193 TYR 0.012 0.002 TYR H 319 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.227 Fit side-chains REVERT: G 478 ASP cc_start: 0.8035 (t0) cc_final: 0.7687 (t0) REVERT: I 246 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: I 471 GLN cc_start: 0.7684 (tp40) cc_final: 0.7416 (tp40) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.2537 time to fit residues: 37.7573 Evaluate side-chains 104 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 55 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120785 restraints weight = 12725.736| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.12 r_work: 0.3188 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10908 Z= 0.147 Angle : 0.497 10.524 14775 Z= 0.255 Chirality : 0.043 0.252 1797 Planarity : 0.003 0.041 1872 Dihedral : 5.913 53.289 1845 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.11 % Allowed : 10.68 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1365 helix: -0.77 (0.27), residues: 411 sheet: -0.24 (0.33), residues: 258 loop : -1.60 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.009 0.001 PHE G 193 TYR 0.011 0.001 TYR H 269 ARG 0.007 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.297 Fit side-chains REVERT: G 478 ASP cc_start: 0.8041 (t0) cc_final: 0.7701 (t0) REVERT: I 246 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: I 421 ASP cc_start: 0.7078 (t0) cc_final: 0.6808 (t0) outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.2574 time to fit residues: 37.5052 Evaluate side-chains 100 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 5.9990 chunk 50 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.0000 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121414 restraints weight = 12768.707| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.10 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10908 Z= 0.138 Angle : 0.489 10.413 14775 Z= 0.250 Chirality : 0.043 0.220 1797 Planarity : 0.003 0.041 1872 Dihedral : 5.174 40.340 1845 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.94 % Allowed : 11.37 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1365 helix: -0.58 (0.27), residues: 411 sheet: -0.10 (0.33), residues: 258 loop : -1.49 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.008 0.001 PHE G 193 TYR 0.011 0.001 TYR H 269 ARG 0.008 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.311 Fit side-chains REVERT: G 478 ASP cc_start: 0.8046 (t0) cc_final: 0.7710 (t0) REVERT: I 246 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: I 471 GLN cc_start: 0.7728 (tp40) cc_final: 0.7514 (tp40) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.2374 time to fit residues: 34.6986 Evaluate side-chains 99 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120475 restraints weight = 12737.791| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3181 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10908 Z= 0.183 Angle : 0.518 11.147 14775 Z= 0.264 Chirality : 0.044 0.191 1797 Planarity : 0.004 0.041 1872 Dihedral : 4.856 31.168 1845 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.11 % Allowed : 12.05 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1365 helix: -0.56 (0.27), residues: 414 sheet: -0.09 (0.33), residues: 258 loop : -1.47 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.010 0.001 PHE G 193 TYR 0.012 0.001 TYR H 385 ARG 0.008 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.228 Fit side-chains REVERT: G 478 ASP cc_start: 0.8079 (t0) cc_final: 0.7767 (t0) REVERT: I 246 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: I 471 GLN cc_start: 0.7763 (tp40) cc_final: 0.7279 (tp40) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.2521 time to fit residues: 35.3124 Evaluate side-chains 103 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 6 optimal weight: 0.0980 chunk 124 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122171 restraints weight = 12740.598| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.09 r_work: 0.3215 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10908 Z= 0.143 Angle : 0.491 11.035 14775 Z= 0.251 Chirality : 0.043 0.166 1797 Planarity : 0.003 0.039 1872 Dihedral : 4.482 22.425 1845 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.03 % Allowed : 12.39 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1365 helix: -0.35 (0.27), residues: 411 sheet: -0.02 (0.33), residues: 258 loop : -1.43 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.008 0.001 PHE G 477 TYR 0.012 0.001 TYR H 269 ARG 0.008 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.391 Fit side-chains REVERT: H 353 ASN cc_start: 0.8275 (t0) cc_final: 0.8052 (t0) REVERT: I 246 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: I 471 GLN cc_start: 0.7736 (tp40) cc_final: 0.7252 (tp40) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.2463 time to fit residues: 36.0154 Evaluate side-chains 103 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119807 restraints weight = 12656.477| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.09 r_work: 0.3145 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10908 Z= 0.216 Angle : 0.531 10.479 14775 Z= 0.272 Chirality : 0.045 0.463 1797 Planarity : 0.004 0.041 1872 Dihedral : 4.457 19.601 1845 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.11 % Allowed : 12.31 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1365 helix: -0.48 (0.27), residues: 414 sheet: -0.11 (0.33), residues: 258 loop : -1.45 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.011 0.001 PHE G 193 TYR 0.012 0.001 TYR H 269 ARG 0.010 0.000 ARG I 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.296 Fit side-chains REVERT: H 440 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7902 (ttp-170) REVERT: I 246 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: I 471 GLN cc_start: 0.7745 (tp40) cc_final: 0.7281 (tp40) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.2619 time to fit residues: 37.3434 Evaluate side-chains 102 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120164 restraints weight = 12650.133| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.09 r_work: 0.3185 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10908 Z= 0.192 Angle : 0.518 10.543 14775 Z= 0.266 Chirality : 0.045 0.466 1797 Planarity : 0.004 0.040 1872 Dihedral : 4.372 19.521 1845 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.94 % Allowed : 12.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.23), residues: 1365 helix: -0.42 (0.27), residues: 414 sheet: -0.12 (0.33), residues: 258 loop : -1.43 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.010 0.001 PHE G 193 TYR 0.012 0.001 TYR H 269 ARG 0.009 0.000 ARG I 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.15 seconds wall clock time: 87 minutes 12.35 seconds (5232.35 seconds total)