Starting phenix.real_space_refine on Thu Jul 31 16:39:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.map" model { file = "/net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt7_43519/07_2025/8vt7_43519.cif" } resolution = 2.66 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8542 2.51 5 N 2320 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13590 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3364 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3370 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3364 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 410} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3370 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.55, per 1000 atoms: 0.78 Number of scatterers: 13590 At special positions: 0 Unit cell: (71.7909, 71.7909, 193.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 10 15.00 Mg 2 11.99 O 2624 8.00 N 2320 7.00 C 8542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 11 sheets defined 55.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.016A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 78 removed outlier: 4.613A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.543A pdb=" N GLU F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.778A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 242 Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 285 through 295 Processing helix chain 'F' and resid 296 through 299 removed outlier: 3.614A pdb=" N MET F 299 " --> pdb=" O ALA F 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 296 through 299' Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.712A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 373 through 392 removed outlier: 4.146A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 402 removed outlier: 4.226A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 402 " --> pdb=" O TYR F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.583A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 removed outlier: 3.855A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 51 removed outlier: 4.210A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 80 removed outlier: 3.688A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 86 removed outlier: 4.580A pdb=" N GLN J 85 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 129 Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.000A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 205 through 216 Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.531A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.631A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 removed outlier: 3.552A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 382 through 400 removed outlier: 4.177A pdb=" N GLU J 386 " --> pdb=" O THR J 382 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 3.791A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.639A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.128A pdb=" N ARG A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 69 through 78 removed outlier: 4.575A pdb=" N MET A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.801A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.842A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU A 194 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 221 through 242 removed outlier: 3.628A pdb=" N LEU A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.663A pdb=" N GLN A 279 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 removed outlier: 3.884A pdb=" N PHE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 373 through 390 removed outlier: 4.169A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.581A pdb=" N PHE A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.607A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.663A pdb=" N THR B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.617A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.693A pdb=" N GLN B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.086A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 244 Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.689A pdb=" N VAL B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.561A pdb=" N TYR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.538A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.127A pdb=" N GLU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.723A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.546A pdb=" N PHE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.050A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.050A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.504A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 92 through 94 removed outlier: 7.989A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU J 3 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE J 135 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE J 5 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL J 137 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE J 7 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS J 139 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL J 9 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS J 200 " --> pdb=" O LYS J 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'J' and resid 351 through 355 removed outlier: 6.680A pdb=" N ASN J 380 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS J 315 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU J 378 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU J 317 " --> pdb=" O CYS J 376 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS J 376 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR J 319 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA J 374 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 removed outlier: 7.991A pdb=" N ILE A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU A 65 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 3 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 133 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL A 5 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A 135 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 7 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA A 9 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ILE A 163 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN A 165 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL A 169 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS A 137 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 164 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR A 200 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 166 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 202 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 168 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR A 199 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N CYS A 201 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N PHE A 270 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 265 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER A 371 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.555A pdb=" N LYS A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.861A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN B 133 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 272 690 hydrogen bonds defined for protein. 1998 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: 4.23 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4511 1.34 - 1.46: 2738 1.46 - 1.58: 6497 1.58 - 1.70: 4 1.70 - 1.82: 150 Bond restraints: 13900 Sorted by residual: bond pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " ideal model delta sigma weight residual 1.610 1.816 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sigma weight residual 1.610 1.816 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O5' GDP A 501 " pdb=" PA GDP A 501 " ideal model delta sigma weight residual 1.610 1.727 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" O5' GDP F 501 " pdb=" PA GDP F 501 " ideal model delta sigma weight residual 1.610 1.727 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O3A GDP F 501 " pdb=" PB GDP F 501 " ideal model delta sigma weight residual 1.610 1.718 -0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 18762 4.02 - 8.05: 78 8.05 - 12.07: 25 12.07 - 16.09: 19 16.09 - 20.11: 4 Bond angle restraints: 18888 Sorted by residual: angle pdb=" PA GDP A 501 " pdb=" O3A GDP A 501 " pdb=" PB GDP A 501 " ideal model delta sigma weight residual 120.50 140.61 -20.11 3.00e+00 1.11e-01 4.50e+01 angle pdb=" PA GDP F 501 " pdb=" O3A GDP F 501 " pdb=" PB GDP F 501 " ideal model delta sigma weight residual 120.50 140.14 -19.64 3.00e+00 1.11e-01 4.28e+01 angle pdb=" O2B GTP J 501 " pdb=" PB GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sigma weight residual 109.50 92.59 16.91 3.00e+00 1.11e-01 3.18e+01 angle pdb=" O2B GTP B 501 " pdb=" PB GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sigma weight residual 109.50 92.96 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C1' GTP J 501 " pdb=" C2' GTP J 501 " pdb=" C3' GTP J 501 " ideal model delta sigma weight residual 111.00 96.12 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 18883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 7936 35.14 - 70.28: 292 70.28 - 105.42: 20 105.42 - 140.55: 3 140.55 - 175.69: 5 Dihedral angle restraints: 8256 sinusoidal: 3276 harmonic: 4980 Sorted by residual: dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 291.08 115.39 175.69 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP J 501 " pdb=" O3A GTP J 501 " pdb=" PB GTP J 501 " pdb=" PA GTP J 501 " ideal model delta sinusoidal sigma weight residual -68.92 102.92 -171.84 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2B GDP A 501 " pdb=" O3A GDP A 501 " pdb=" PB GDP A 501 " pdb=" PA GDP A 501 " ideal model delta sinusoidal sigma weight residual 180.00 10.34 169.66 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 8253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1879 0.070 - 0.140: 180 0.140 - 0.210: 3 0.210 - 0.280: 6 0.280 - 0.350: 4 Chirality restraints: 2072 Sorted by residual: chirality pdb=" C2' GDP F 501 " pdb=" C3' GDP F 501 " pdb=" O2' GDP F 501 " pdb=" C1' GDP F 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.86 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C2' GDP A 501 " pdb=" C3' GDP A 501 " pdb=" O2' GDP A 501 " pdb=" C1' GDP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.85 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' GTP J 501 " pdb=" C2' GTP J 501 " pdb=" C4' GTP J 501 " pdb=" O3' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.80 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2069 not shown) Planarity restraints: 2458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 236 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C SER B 236 " 0.032 2.00e-02 2.50e+03 pdb=" O SER B 236 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 237 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C ARG A 380 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 380 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 381 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 383 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C GLU A 383 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A 383 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN A 384 " 0.009 2.00e-02 2.50e+03 ... (remaining 2455 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 62 2.48 - 3.09: 9936 3.09 - 3.69: 21274 3.69 - 4.30: 32904 4.30 - 4.90: 56727 Nonbonded interactions: 120903 Sorted by model distance: nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 1.877 2.170 nonbonded pdb=" O1G GTP B 501 " pdb="MG MG B 502 " model vdw 1.879 2.170 nonbonded pdb=" O ARG F 276 " pdb=" NE ARG F 276 " model vdw 2.050 3.120 nonbonded pdb=" OH TYR J 224 " pdb=" O2' GTP J 501 " model vdw 2.161 3.040 nonbonded pdb=" OG1 THR F 238 " pdb=" NH2 ARG F 241 " model vdw 2.181 3.120 ... (remaining 120898 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'J' } 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: 8.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 36.060 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.006 0.206 13900 Z= 0.305 Angle : 0.872 20.114 18888 Z= 0.354 Chirality : 0.046 0.350 2072 Planarity : 0.004 0.037 2458 Dihedral : 18.190 175.693 5060 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 17.10 % Favored : 81.32 % 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: 0.60 (0.21), residues: 1710 helix: 1.29 (0.19), residues: 788 sheet: -0.55 (0.33), residues: 250 loop : -0.16 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 21 HIS 0.003 0.001 HIS J 88 PHE 0.020 0.001 PHE J 49 TYR 0.011 0.001 TYR B 172 ARG 0.004 0.000 ARG F 359 Details of bonding type rmsd hydrogen bonds : bond 0.14133 ( 685) hydrogen bonds : angle 6.55903 ( 1998) covalent geometry : bond 0.00637 (13900) covalent geometry : angle 0.87215 (18888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: F 45 GLU cc_start: 0.8005 (tt0) cc_final: 0.7514 (tt0) REVERT: F 188 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8356 (m) REVERT: F 330 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7158 (mpm) REVERT: J 377 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7971 (ttm) REVERT: A 88 ASP cc_start: 0.8651 (t0) cc_final: 0.8243 (t0) REVERT: A 320 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8225 (tpp80) REVERT: A 406 MET cc_start: 0.7591 (tpp) cc_final: 0.7230 (tpp) REVERT: B 155 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 156 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7722 (mmm160) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 1.4703 time to fit residues: 208.0898 Evaluate side-chains 132 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 379 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN J 101 ASN B 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.092700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077468 restraints weight = 18659.117| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.17 r_work: 0.3068 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13900 Z= 0.169 Angle : 0.555 7.579 18888 Z= 0.279 Chirality : 0.044 0.162 2072 Planarity : 0.004 0.043 2458 Dihedral : 12.289 159.085 1962 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 16.07 % Favored : 81.52 % 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: 1.03 (0.21), residues: 1710 helix: 1.59 (0.19), residues: 822 sheet: -0.19 (0.33), residues: 256 loop : -0.03 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 21 HIS 0.003 0.001 HIS B 107 PHE 0.014 0.001 PHE F 367 TYR 0.009 0.001 TYR F 59 ARG 0.003 0.000 ARG F 318 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 685) hydrogen bonds : angle 4.92464 ( 1998) covalent geometry : bond 0.00385 (13900) covalent geometry : angle 0.55522 (18888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: F 45 GLU cc_start: 0.8094 (tt0) cc_final: 0.7743 (tp30) REVERT: J 339 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7741 (tpp-160) REVERT: J 377 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.9002 (ttp) REVERT: J 437 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8193 (p) REVERT: A 88 ASP cc_start: 0.8840 (t0) cc_final: 0.8491 (t0) REVERT: A 406 MET cc_start: 0.7782 (tpp) cc_final: 0.7354 (tpp) REVERT: B 155 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8395 (mt-10) REVERT: B 326 LYS cc_start: 0.4551 (tptm) cc_final: 0.4224 (tptm) outliers start: 35 outliers final: 6 residues processed: 137 average time/residue: 1.3416 time to fit residues: 200.9790 Evaluate side-chains 116 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 71 optimal weight: 0.0010 chunk 74 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077664 restraints weight = 19918.324| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.29 r_work: 0.3056 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13900 Z= 0.154 Angle : 0.525 7.900 18888 Z= 0.264 Chirality : 0.043 0.140 2072 Planarity : 0.004 0.038 2458 Dihedral : 11.634 179.128 1927 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.79 % Allowed : 17.31 % Favored : 80.91 % 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: 1.05 (0.21), residues: 1710 helix: 1.63 (0.18), residues: 822 sheet: -0.13 (0.33), residues: 256 loop : -0.06 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 21 HIS 0.003 0.001 HIS B 107 PHE 0.019 0.001 PHE J 49 TYR 0.008 0.001 TYR F 425 ARG 0.010 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 685) hydrogen bonds : angle 4.72090 ( 1998) covalent geometry : bond 0.00349 (13900) covalent geometry : angle 0.52461 (18888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: F 45 GLU cc_start: 0.7830 (tt0) cc_final: 0.7342 (tp30) REVERT: F 322 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8103 (p) REVERT: J 295 CYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8137 (m) REVERT: J 339 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7405 (tpp-160) REVERT: A 88 ASP cc_start: 0.8790 (t0) cc_final: 0.8347 (t0) REVERT: A 143 THR cc_start: 0.8320 (m) cc_final: 0.8092 (m) REVERT: A 276 ARG cc_start: 0.8118 (tmt170) cc_final: 0.7899 (tpt170) REVERT: A 320 ARG cc_start: 0.8610 (tpp80) cc_final: 0.8321 (tpp-160) REVERT: A 406 MET cc_start: 0.7540 (tpp) cc_final: 0.7024 (tpp) REVERT: B 155 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 326 LYS cc_start: 0.4227 (tptm) cc_final: 0.3932 (tptm) REVERT: B 425 MET cc_start: 0.7748 (mmm) cc_final: 0.7290 (mmm) outliers start: 26 outliers final: 6 residues processed: 132 average time/residue: 1.3930 time to fit residues: 201.2954 Evaluate side-chains 117 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 112 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.092368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076987 restraints weight = 19884.606| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.28 r_work: 0.3044 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13900 Z= 0.186 Angle : 0.548 8.676 18888 Z= 0.274 Chirality : 0.044 0.145 2072 Planarity : 0.004 0.040 2458 Dihedral : 11.433 179.144 1920 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.13 % Allowed : 17.38 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.20), residues: 1710 helix: 1.58 (0.18), residues: 818 sheet: -0.21 (0.33), residues: 262 loop : -0.19 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 21 HIS 0.004 0.001 HIS A 105 PHE 0.017 0.001 PHE J 49 TYR 0.010 0.001 TYR F 425 ARG 0.005 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 685) hydrogen bonds : angle 4.70532 ( 1998) covalent geometry : bond 0.00429 (13900) covalent geometry : angle 0.54769 (18888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: F 194 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8115 (mt-10) REVERT: F 322 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8109 (p) REVERT: J 295 CYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8161 (m) REVERT: J 339 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7371 (tpm170) REVERT: J 377 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8559 (ttp) REVERT: A 88 ASP cc_start: 0.8782 (t0) cc_final: 0.8365 (t0) REVERT: A 320 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8325 (tpp-160) REVERT: A 406 MET cc_start: 0.7547 (tpp) cc_final: 0.7333 (tpp) REVERT: B 155 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: B 326 LYS cc_start: 0.4054 (tptm) cc_final: 0.3723 (tptm) outliers start: 31 outliers final: 14 residues processed: 133 average time/residue: 1.3372 time to fit residues: 195.3067 Evaluate side-chains 127 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.092264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076877 restraints weight = 20082.139| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.30 r_work: 0.3042 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13900 Z= 0.189 Angle : 0.542 7.967 18888 Z= 0.271 Chirality : 0.044 0.150 2072 Planarity : 0.004 0.040 2458 Dihedral : 11.381 179.760 1920 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.47 % Allowed : 17.51 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1710 helix: 1.51 (0.18), residues: 822 sheet: -0.11 (0.33), residues: 256 loop : -0.18 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 21 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.001 PHE J 49 TYR 0.011 0.001 TYR J 161 ARG 0.006 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 685) hydrogen bonds : angle 4.68392 ( 1998) covalent geometry : bond 0.00435 (13900) covalent geometry : angle 0.54220 (18888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: F 188 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8314 (m) REVERT: F 194 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 280 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: F 322 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8118 (p) REVERT: J 161 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: J 295 CYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8564 (m) REVERT: J 339 ARG cc_start: 0.7811 (tpp-160) cc_final: 0.7386 (tpm170) REVERT: J 377 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8529 (ttp) REVERT: A 88 ASP cc_start: 0.8808 (t0) cc_final: 0.8384 (t0) REVERT: A 288 GLU cc_start: 0.7497 (tp30) cc_final: 0.7296 (tp30) REVERT: A 320 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8322 (tpp-160) REVERT: B 155 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: B 326 LYS cc_start: 0.3979 (tptm) cc_final: 0.3649 (tptm) outliers start: 36 outliers final: 17 residues processed: 145 average time/residue: 1.3069 time to fit residues: 209.6307 Evaluate side-chains 137 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.091972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077101 restraints weight = 19057.021| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.15 r_work: 0.3059 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13900 Z= 0.208 Angle : 0.566 9.301 18888 Z= 0.283 Chirality : 0.045 0.149 2072 Planarity : 0.004 0.042 2458 Dihedral : 11.377 179.687 1920 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.40 % Allowed : 18.13 % Favored : 79.46 % 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: 0.83 (0.20), residues: 1710 helix: 1.46 (0.18), residues: 824 sheet: -0.11 (0.33), residues: 256 loop : -0.28 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 21 HIS 0.004 0.001 HIS A 105 PHE 0.019 0.001 PHE J 49 TYR 0.011 0.001 TYR F 425 ARG 0.003 0.000 ARG F 318 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 685) hydrogen bonds : angle 4.71537 ( 1998) covalent geometry : bond 0.00482 (13900) covalent geometry : angle 0.56638 (18888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: F 164 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8814 (ttp) REVERT: F 188 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8824 (m) REVERT: F 194 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8240 (mt-10) REVERT: F 280 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: F 322 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8627 (p) REVERT: J 161 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: J 295 CYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8840 (m) REVERT: J 339 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7681 (tpm170) REVERT: J 377 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8786 (ttp) REVERT: J 392 ASP cc_start: 0.8696 (m-30) cc_final: 0.8099 (m-30) REVERT: A 88 ASP cc_start: 0.8863 (t0) cc_final: 0.8528 (t0) REVERT: A 320 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8391 (tpp-160) REVERT: A 406 MET cc_start: 0.7850 (tpp) cc_final: 0.7366 (tpp) REVERT: B 155 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: B 326 LYS cc_start: 0.4852 (tptm) cc_final: 0.4431 (tptm) outliers start: 35 outliers final: 18 residues processed: 140 average time/residue: 1.2845 time to fit residues: 197.6562 Evaluate side-chains 138 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 110 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076905 restraints weight = 18971.696| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.15 r_work: 0.3054 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13900 Z= 0.216 Angle : 0.567 7.926 18888 Z= 0.284 Chirality : 0.045 0.152 2072 Planarity : 0.004 0.042 2458 Dihedral : 11.457 179.393 1920 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 18.48 % Favored : 79.33 % 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: 0.77 (0.20), residues: 1710 helix: 1.42 (0.18), residues: 824 sheet: -0.13 (0.33), residues: 256 loop : -0.31 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 21 HIS 0.004 0.001 HIS A 105 PHE 0.023 0.002 PHE J 49 TYR 0.012 0.001 TYR F 425 ARG 0.003 0.000 ARG F 359 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 685) hydrogen bonds : angle 4.73928 ( 1998) covalent geometry : bond 0.00503 (13900) covalent geometry : angle 0.56743 (18888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 2.069 Fit side-chains revert: symmetry clash REVERT: F 188 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8819 (m) REVERT: F 194 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8232 (mt-10) REVERT: F 280 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: F 322 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8663 (p) REVERT: J 161 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: J 295 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8814 (m) REVERT: J 339 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7690 (tpm170) REVERT: J 377 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8854 (ttp) REVERT: J 392 ASP cc_start: 0.8712 (m-30) cc_final: 0.8101 (m-30) REVERT: A 88 ASP cc_start: 0.8864 (t0) cc_final: 0.8527 (t0) REVERT: A 114 ASP cc_start: 0.8021 (p0) cc_final: 0.7813 (p0) REVERT: A 320 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8400 (tpp-160) REVERT: A 406 MET cc_start: 0.7817 (tpp) cc_final: 0.7275 (tpp) REVERT: B 155 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: B 297 GLU cc_start: 0.7606 (tp30) cc_final: 0.7385 (tp30) REVERT: B 326 LYS cc_start: 0.4810 (tptm) cc_final: 0.4424 (tptm) outliers start: 32 outliers final: 20 residues processed: 140 average time/residue: 1.2307 time to fit residues: 189.9813 Evaluate side-chains 140 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 47 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 61 optimal weight: 0.2980 chunk 139 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 150 optimal weight: 0.0570 chunk 71 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079690 restraints weight = 18699.634| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.23 r_work: 0.3103 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13900 Z= 0.123 Angle : 0.520 8.785 18888 Z= 0.258 Chirality : 0.042 0.148 2072 Planarity : 0.004 0.041 2458 Dihedral : 11.337 176.222 1920 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.65 % Allowed : 19.57 % Favored : 78.78 % 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: 0.90 (0.20), residues: 1710 helix: 1.60 (0.18), residues: 820 sheet: -0.19 (0.32), residues: 266 loop : -0.29 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 21 HIS 0.002 0.001 HIS B 107 PHE 0.016 0.001 PHE J 49 TYR 0.012 0.001 TYR J 161 ARG 0.009 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 685) hydrogen bonds : angle 4.56025 ( 1998) covalent geometry : bond 0.00268 (13900) covalent geometry : angle 0.51965 (18888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 188 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8776 (m) REVERT: F 194 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8232 (mt-10) REVERT: F 322 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8617 (p) REVERT: F 406 MET cc_start: 0.7662 (tpp) cc_final: 0.7360 (tpp) REVERT: J 161 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: J 295 CYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8848 (m) REVERT: J 339 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7652 (tpm170) REVERT: J 377 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8724 (ttp) REVERT: J 392 ASP cc_start: 0.8678 (m-30) cc_final: 0.8107 (m-30) REVERT: A 88 ASP cc_start: 0.8856 (t0) cc_final: 0.8519 (t0) REVERT: A 276 ARG cc_start: 0.8208 (tmt170) cc_final: 0.7803 (tpm-80) REVERT: A 320 ARG cc_start: 0.8655 (tpp80) cc_final: 0.8362 (tpp-160) REVERT: A 376 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7949 (mm-30) REVERT: A 406 MET cc_start: 0.7904 (tpp) cc_final: 0.7331 (tpp) REVERT: B 297 GLU cc_start: 0.7536 (tp30) cc_final: 0.7306 (tp30) REVERT: B 326 LYS cc_start: 0.4587 (tptm) cc_final: 0.4146 (tptm) outliers start: 24 outliers final: 10 residues processed: 142 average time/residue: 1.3535 time to fit residues: 210.5802 Evaluate side-chains 130 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 146 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077848 restraints weight = 19818.625| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.28 r_work: 0.3057 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13900 Z= 0.169 Angle : 0.548 9.348 18888 Z= 0.272 Chirality : 0.044 0.149 2072 Planarity : 0.004 0.043 2458 Dihedral : 11.369 177.218 1920 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.30 % Allowed : 20.26 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1710 helix: 1.54 (0.18), residues: 822 sheet: -0.08 (0.33), residues: 256 loop : -0.22 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 21 HIS 0.003 0.001 HIS A 105 PHE 0.015 0.001 PHE J 49 TYR 0.011 0.001 TYR J 161 ARG 0.012 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 685) hydrogen bonds : angle 4.59726 ( 1998) covalent geometry : bond 0.00389 (13900) covalent geometry : angle 0.54772 (18888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: F 188 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8365 (m) REVERT: F 194 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8068 (mt-10) REVERT: F 322 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8191 (p) REVERT: F 406 MET cc_start: 0.7475 (tpp) cc_final: 0.7134 (tpp) REVERT: J 161 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: J 295 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8581 (m) REVERT: J 339 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7433 (tpm170) REVERT: J 377 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8544 (ttp) REVERT: J 392 ASP cc_start: 0.8567 (m-30) cc_final: 0.7831 (m-30) REVERT: A 88 ASP cc_start: 0.8813 (t0) cc_final: 0.8405 (t0) REVERT: A 320 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8289 (tpp-160) REVERT: A 406 MET cc_start: 0.7720 (tpp) cc_final: 0.7518 (tpp) REVERT: B 98 ASP cc_start: 0.8312 (p0) cc_final: 0.8042 (p0) REVERT: B 155 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 297 GLU cc_start: 0.7210 (tp30) cc_final: 0.6982 (tp30) REVERT: B 326 LYS cc_start: 0.4010 (tptm) cc_final: 0.3641 (tptm) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 1.3046 time to fit residues: 184.7355 Evaluate side-chains 131 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.093754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078402 restraints weight = 19844.395| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.29 r_work: 0.3068 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13900 Z= 0.154 Angle : 0.551 10.108 18888 Z= 0.273 Chirality : 0.043 0.152 2072 Planarity : 0.004 0.041 2458 Dihedral : 11.386 176.796 1920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 20.05 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1710 helix: 1.56 (0.18), residues: 820 sheet: -0.22 (0.32), residues: 274 loop : -0.24 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 21 HIS 0.003 0.001 HIS B 107 PHE 0.020 0.001 PHE J 49 TYR 0.011 0.001 TYR J 161 ARG 0.012 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 685) hydrogen bonds : angle 4.57948 ( 1998) covalent geometry : bond 0.00351 (13900) covalent geometry : angle 0.55125 (18888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: F 188 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8295 (m) REVERT: F 194 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8033 (mt-10) REVERT: F 322 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8125 (p) REVERT: F 406 MET cc_start: 0.7411 (tpp) cc_final: 0.7101 (tpp) REVERT: J 161 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: J 295 CYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8548 (m) REVERT: J 339 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7410 (tpm170) REVERT: J 377 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8514 (ttp) REVERT: J 392 ASP cc_start: 0.8532 (m-30) cc_final: 0.7788 (m-30) REVERT: A 88 ASP cc_start: 0.8800 (t0) cc_final: 0.8407 (t0) REVERT: A 143 THR cc_start: 0.8318 (m) cc_final: 0.8017 (m) REVERT: A 320 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8277 (tpp-160) REVERT: A 376 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7554 (mm-30) REVERT: A 406 MET cc_start: 0.7689 (tpp) cc_final: 0.7482 (tpp) REVERT: B 98 ASP cc_start: 0.8293 (p0) cc_final: 0.8015 (p0) REVERT: B 155 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 297 GLU cc_start: 0.7167 (tp30) cc_final: 0.6955 (tp30) REVERT: B 326 LYS cc_start: 0.3748 (tptm) cc_final: 0.3394 (tptm) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 1.4582 time to fit residues: 214.0303 Evaluate side-chains 131 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 405 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 295 CYS Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.091065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075555 restraints weight = 20334.706| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.40 r_work: 0.3010 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13900 Z= 0.222 Angle : 0.580 9.527 18888 Z= 0.290 Chirality : 0.045 0.152 2072 Planarity : 0.004 0.041 2458 Dihedral : 11.445 178.210 1920 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.44 % Allowed : 20.26 % Favored : 78.30 % 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: 0.80 (0.20), residues: 1710 helix: 1.45 (0.18), residues: 822 sheet: -0.14 (0.32), residues: 260 loop : -0.29 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 21 HIS 0.004 0.001 HIS A 105 PHE 0.021 0.002 PHE J 49 TYR 0.012 0.001 TYR F 425 ARG 0.011 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 685) hydrogen bonds : angle 4.69536 ( 1998) covalent geometry : bond 0.00518 (13900) covalent geometry : angle 0.58009 (18888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8568.87 seconds wall clock time: 147 minutes 16.94 seconds (8836.94 seconds total)