Starting phenix.real_space_refine on Wed May 28 18:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478.map" model { file = "/net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uqv_42478/05_2025/8uqv_42478_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 64 5.16 5 C 11488 2.51 5 N 3072 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18024 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "B" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "C" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "D" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 9.62, per 1000 atoms: 0.53 Number of scatterers: 18024 At special positions: 0 Unit cell: (88.14, 141.25, 135.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 64 16.00 O 3396 8.00 N 3072 7.00 C 11488 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 28.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.585A pdb=" N GLY A 114 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.814A pdb=" N PHE A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.934A pdb=" N SER A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 removed outlier: 4.363A pdb=" N ASP A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.179A pdb=" N LEU A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 256 through 272 removed outlier: 3.787A pdb=" N PHE A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.572A pdb=" N PHE A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 4.607A pdb=" N ILE A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.699A pdb=" N MET A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.727A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.341A pdb=" N GLN A 547 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.792A pdb=" N LEU B 71 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.861A pdb=" N LEU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.710A pdb=" N GLY B 114 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.787A pdb=" N ARG B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.510A pdb=" N ALA B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 256 through 271 removed outlier: 3.662A pdb=" N PHE B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.080A pdb=" N PHE B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 318 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 4.237A pdb=" N ILE B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.518A pdb=" N ASP B 363 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.848A pdb=" N GLU B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.816A pdb=" N ASP B 430 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 431 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 446 Processing helix chain 'B' and resid 480 through 493 removed outlier: 3.809A pdb=" N ARG B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 4.359A pdb=" N GLN B 547 " --> pdb=" O ASP B 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 74 through 81 removed outlier: 3.742A pdb=" N LEU C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.823A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.663A pdb=" N MET C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.830A pdb=" N TRP C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 256 through 271 Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.903A pdb=" N VAL C 289 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 310 through 321 removed outlier: 4.368A pdb=" N PHE C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 354 through 358 removed outlier: 4.465A pdb=" N VAL C 357 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 358 " --> pdb=" O GLU C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 358' Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.933A pdb=" N ARG C 362 " --> pdb=" O ASP C 359 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP C 363 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.548A pdb=" N LEU C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 404 removed outlier: 3.593A pdb=" N LEU C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 446 Processing helix chain 'C' and resid 480 through 495 removed outlier: 3.635A pdb=" N ARG C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 495 " --> pdb=" O VAL C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.437A pdb=" N GLN C 547 " --> pdb=" O ASP C 544 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 549 " --> pdb=" O GLN C 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.961A pdb=" N ASP D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 82 Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.558A pdb=" N GLY D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 146 through 154 removed outlier: 4.067A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 231 removed outlier: 3.972A pdb=" N ILE D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY D 231 " --> pdb=" O TRP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 254 through 271 removed outlier: 4.021A pdb=" N HIS D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 310 through 320 removed outlier: 4.333A pdb=" N PHE D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.981A pdb=" N ILE D 329 " --> pdb=" O PRO D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 369 removed outlier: 3.841A pdb=" N ALA D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'D' and resid 545 through 549 removed outlier: 3.953A pdb=" N THR D 549 " --> pdb=" O GLN D 546 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135 removed outlier: 5.986A pdb=" N TYR A 50 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 49 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE A 344 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N TYR A 413 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 138 removed outlier: 7.295A pdb=" N LEU A 137 " --> pdb=" O ALA A 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 516 removed outlier: 3.619A pdb=" N VAL A 531 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 580 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AA5, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.419A pdb=" N ILE B 86 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP B 136 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 88 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL B 138 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR B 50 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE B 49 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 344 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N TYR B 413 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AA7, first strand: chain 'B' and resid 513 through 516 removed outlier: 3.858A pdb=" N CYS B 530 " --> pdb=" O TYR B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AA9, first strand: chain 'C' and resid 132 through 135 removed outlier: 6.002A pdb=" N TYR C 50 " --> pdb=" O TRP C 87 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 49 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 167 Processing sheet with id=AB2, first strand: chain 'C' and resid 514 through 516 Processing sheet with id=AB3, first strand: chain 'C' and resid 539 through 542 Processing sheet with id=AB4, first strand: chain 'D' and resid 235 through 238 removed outlier: 8.600A pdb=" N ARG D 236 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR D 135 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA D 238 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 137 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AB6, first strand: chain 'D' and resid 504 through 505 removed outlier: 3.670A pdb=" N GLN D 504 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 539 through 543 359 hydrogen bonds defined for protein. 915 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: 4.89 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4691 1.33 - 1.45: 3896 1.45 - 1.57: 9797 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 18496 Sorted by residual: bond pdb=" N PRO B 214 " pdb=" CD PRO B 214 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" N2 XVC A 602 " pdb=" N3 XVC A 602 " ideal model delta sigma weight residual 1.125 1.215 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" N2 XVC C 602 " pdb=" N3 XVC C 602 " ideal model delta sigma weight residual 1.125 1.215 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" N2 XVC D 602 " pdb=" N3 XVC D 602 " ideal model delta sigma weight residual 1.125 1.213 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" N2 XVC B 602 " pdb=" N3 XVC B 602 " ideal model delta sigma weight residual 1.125 1.212 -0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 18491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.68: 25232 12.68 - 25.35: 0 25.35 - 38.03: 0 38.03 - 50.71: 0 50.71 - 63.39: 4 Bond angle restraints: 25236 Sorted by residual: angle pdb=" C6 XVC C 602 " pdb=" N1 XVC C 602 " pdb=" N2 XVC C 602 " ideal model delta sigma weight residual 116.55 179.94 -63.39 3.00e+00 1.11e-01 4.46e+02 angle pdb=" C6 XVC D 602 " pdb=" N1 XVC D 602 " pdb=" N2 XVC D 602 " ideal model delta sigma weight residual 116.55 178.65 -62.10 3.00e+00 1.11e-01 4.28e+02 angle pdb=" C6 XVC B 602 " pdb=" N1 XVC B 602 " pdb=" N2 XVC B 602 " ideal model delta sigma weight residual 116.55 178.62 -62.07 3.00e+00 1.11e-01 4.28e+02 angle pdb=" C6 XVC A 602 " pdb=" N1 XVC A 602 " pdb=" N2 XVC A 602 " ideal model delta sigma weight residual 116.55 176.23 -59.68 3.00e+00 1.11e-01 3.96e+02 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 113.20 108.93 4.27 9.60e-01 1.09e+00 1.98e+01 ... (remaining 25231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 10203 25.74 - 51.48: 616 51.48 - 77.23: 59 77.23 - 102.97: 32 102.97 - 128.71: 14 Dihedral angle restraints: 10924 sinusoidal: 4576 harmonic: 6348 Sorted by residual: dihedral pdb=" CA GLU B 361 " pdb=" C GLU B 361 " pdb=" N ARG B 362 " pdb=" CA ARG B 362 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR B 516 " pdb=" C TYR B 516 " pdb=" N VAL B 517 " pdb=" CA VAL B 517 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLN A 217 " pdb=" C GLN A 217 " pdb=" N GLU A 218 " pdb=" CA GLU A 218 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 10921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2115 0.054 - 0.109: 455 0.109 - 0.163: 53 0.163 - 0.218: 6 0.218 - 0.272: 3 Chirality restraints: 2632 Sorted by residual: chirality pdb=" C1 GLC A 601 " pdb=" C2 GLC A 601 " pdb=" O1 GLC A 601 " pdb=" O5 GLC A 601 " both_signs ideal model delta sigma weight residual False -2.04 -2.31 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 GLC B 601 " pdb=" C2 GLC B 601 " pdb=" O1 GLC B 601 " pdb=" O5 GLC B 601 " both_signs ideal model delta sigma weight residual False -2.04 -2.31 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 GLC C 601 " pdb=" C2 GLC C 601 " pdb=" O1 GLC C 601 " pdb=" O5 GLC C 601 " both_signs ideal model delta sigma weight residual False -2.04 -2.30 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2629 not shown) Planarity restraints: 3344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 191 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO C 192 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 254 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 255 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 166 " -0.010 2.00e-02 2.50e+03 1.22e-02 3.70e+00 pdb=" CG TRP A 166 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 166 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 166 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 166 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 166 " -0.001 2.00e-02 2.50e+03 ... (remaining 3341 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 86 2.35 - 2.98: 11266 2.98 - 3.62: 24500 3.62 - 4.26: 39199 4.26 - 4.90: 67646 Nonbonded interactions: 142697 Sorted by model distance: nonbonded pdb=" O PRO D 192 " pdb=" NH1 ARG D 195 " model vdw 1.708 3.120 nonbonded pdb=" OE2 GLU A 280 " pdb=" O3 XVC A 602 " model vdw 1.874 3.040 nonbonded pdb=" OD1 ASN B 253 " pdb=" OH TYR B 291 " model vdw 1.887 3.040 nonbonded pdb=" O ASN A 140 " pdb=" OD1 ASN A 140 " model vdw 1.932 3.040 nonbonded pdb=" CD GLU A 280 " pdb=" O3 XVC A 602 " model vdw 1.941 3.270 ... (remaining 142692 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.180 Process input model: 40.540 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 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 : 0.005 0.090 18500 Z= 0.204 Angle : 0.996 63.386 25236 Z= 0.413 Chirality : 0.045 0.272 2632 Planarity : 0.005 0.085 3344 Dihedral : 16.965 128.710 6860 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 46.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.52 % Favored : 82.43 % Rotamer: Outliers : 0.05 % Allowed : 0.21 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.17), residues: 2180 helix: -1.41 (0.23), residues: 492 sheet: -2.74 (0.31), residues: 288 loop : -2.91 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 166 HIS 0.012 0.001 HIS D 307 PHE 0.016 0.001 PHE C 503 TYR 0.030 0.002 TYR A 101 ARG 0.004 0.000 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.19574 ( 359) hydrogen bonds : angle 7.19982 ( 915) covalent geometry : bond 0.00453 (18496) covalent geometry : angle 0.99569 (25236) Misc. bond : bond 0.02782 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.7269 (t) cc_final: 0.7005 (t) REVERT: A 556 LEU cc_start: 0.6091 (mt) cc_final: 0.5080 (mt) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.3290 time to fit residues: 237.6463 Evaluate side-chains 299 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0270 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 510 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 253 ASN C 443 ASN ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 470 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152141 restraints weight = 22921.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155008 restraints weight = 13480.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.156931 restraints weight = 8933.733| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18500 Z= 0.199 Angle : 0.837 10.656 25236 Z= 0.419 Chirality : 0.051 0.266 2632 Planarity : 0.007 0.099 3344 Dihedral : 8.739 102.582 2628 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.42 % Favored : 88.49 % Rotamer: Outliers : 3.01 % Allowed : 12.82 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.17), residues: 2180 helix: -1.67 (0.22), residues: 508 sheet: -2.67 (0.28), residues: 344 loop : -2.55 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 199 HIS 0.014 0.002 HIS B 307 PHE 0.026 0.002 PHE B 399 TYR 0.037 0.002 TYR D 173 ARG 0.011 0.001 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 359) hydrogen bonds : angle 5.16833 ( 915) covalent geometry : bond 0.00433 (18496) covalent geometry : angle 0.83663 (25236) Misc. bond : bond 0.00200 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 339 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ILE cc_start: 0.5715 (tt) cc_final: 0.5464 (tt) REVERT: A 339 MET cc_start: 0.6099 (tpp) cc_final: 0.5728 (tpp) REVERT: A 356 MET cc_start: 0.4443 (ppp) cc_final: 0.3660 (ppp) outliers start: 57 outliers final: 28 residues processed: 377 average time/residue: 0.2879 time to fit residues: 165.3917 Evaluate side-chains 299 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 9 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS B 200 HIS B 205 HIS B 258 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN ** D 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151711 restraints weight = 23022.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154502 restraints weight = 13849.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156410 restraints weight = 9330.789| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18500 Z= 0.185 Angle : 0.739 10.593 25236 Z= 0.375 Chirality : 0.048 0.202 2632 Planarity : 0.006 0.065 3344 Dihedral : 6.893 111.034 2628 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.96 % Favored : 88.94 % Rotamer: Outliers : 4.27 % Allowed : 15.30 % Favored : 80.43 % 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: -3.41 (0.17), residues: 2180 helix: -1.54 (0.22), residues: 512 sheet: -2.72 (0.26), residues: 412 loop : -2.48 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 548 HIS 0.009 0.001 HIS B 200 PHE 0.025 0.002 PHE B 190 TYR 0.021 0.002 TYR A 198 ARG 0.013 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 359) hydrogen bonds : angle 5.03913 ( 915) covalent geometry : bond 0.00436 (18496) covalent geometry : angle 0.73889 (25236) Misc. bond : bond 0.00172 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 333 time to evaluate : 1.846 Fit side-chains REVERT: A 67 ASP cc_start: 0.5990 (t0) cc_final: 0.5780 (t0) REVERT: A 195 ARG cc_start: 0.6142 (mtm-85) cc_final: 0.5794 (mmt180) REVERT: A 334 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8320 (Cg_exo) REVERT: A 356 MET cc_start: 0.4287 (ppp) cc_final: 0.3807 (ppp) REVERT: B 163 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 289 VAL cc_start: 0.7850 (t) cc_final: 0.7602 (p) REVERT: C 396 ILE cc_start: 0.8690 (mm) cc_final: 0.8309 (mt) REVERT: D 106 PHE cc_start: 0.7153 (m-10) cc_final: 0.6939 (m-10) REVERT: D 365 MET cc_start: 0.6178 (ttp) cc_final: 0.5893 (ttt) REVERT: D 381 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6226 (mt) outliers start: 81 outliers final: 36 residues processed: 389 average time/residue: 0.2852 time to fit residues: 169.5832 Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 0.0980 chunk 148 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152523 restraints weight = 23372.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155873 restraints weight = 13344.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158131 restraints weight = 8660.269| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18500 Z= 0.151 Angle : 0.687 11.202 25236 Z= 0.345 Chirality : 0.046 0.198 2632 Planarity : 0.005 0.063 3344 Dihedral : 6.349 119.403 2628 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.33 % Favored : 88.62 % Rotamer: Outliers : 4.17 % Allowed : 16.98 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.18), residues: 2180 helix: -1.33 (0.22), residues: 512 sheet: -2.69 (0.25), residues: 408 loop : -2.33 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 199 HIS 0.011 0.001 HIS B 307 PHE 0.020 0.002 PHE A 484 TYR 0.020 0.001 TYR D 173 ARG 0.017 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 359) hydrogen bonds : angle 4.78743 ( 915) covalent geometry : bond 0.00360 (18496) covalent geometry : angle 0.68721 (25236) Misc. bond : bond 0.00056 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 274 time to evaluate : 2.390 Fit side-chains REVERT: A 86 ILE cc_start: 0.7907 (mt) cc_final: 0.7555 (mt) REVERT: A 195 ARG cc_start: 0.6878 (mtm-85) cc_final: 0.6300 (mmt180) REVERT: A 356 MET cc_start: 0.4374 (ppp) cc_final: 0.4087 (ppp) REVERT: A 437 GLN cc_start: 0.8334 (mt0) cc_final: 0.8102 (mt0) REVERT: B 83 ILE cc_start: 0.7794 (mm) cc_final: 0.7563 (mm) REVERT: B 368 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6254 (mm-30) REVERT: B 472 GLU cc_start: 0.7011 (tp30) cc_final: 0.6637 (tt0) REVERT: C 396 ILE cc_start: 0.8689 (mm) cc_final: 0.8307 (mt) REVERT: D 365 MET cc_start: 0.6298 (ttp) cc_final: 0.5962 (ttt) outliers start: 79 outliers final: 53 residues processed: 330 average time/residue: 0.2515 time to fit residues: 133.1132 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 166 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B 550 ASN B 577 HIS C 140 ASN C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.163904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151127 restraints weight = 23541.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154273 restraints weight = 13740.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156409 restraints weight = 9095.850| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18500 Z= 0.152 Angle : 0.678 12.508 25236 Z= 0.343 Chirality : 0.046 0.202 2632 Planarity : 0.005 0.062 3344 Dihedral : 5.992 120.535 2628 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.92 % Favored : 89.04 % Rotamer: Outliers : 4.32 % Allowed : 18.14 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 2180 helix: -1.24 (0.22), residues: 508 sheet: -2.41 (0.28), residues: 352 loop : -2.15 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 43 HIS 0.006 0.001 HIS B 349 PHE 0.023 0.002 PHE A 484 TYR 0.018 0.001 TYR D 173 ARG 0.006 0.001 ARG D 393 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 359) hydrogen bonds : angle 4.68180 ( 915) covalent geometry : bond 0.00360 (18496) covalent geometry : angle 0.67849 (25236) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 1.924 Fit side-chains REVERT: A 195 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6556 (mmt180) REVERT: A 262 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7708 (mttp) REVERT: A 356 MET cc_start: 0.4937 (ppp) cc_final: 0.4550 (ppp) REVERT: A 414 TYR cc_start: 0.8678 (p90) cc_final: 0.8463 (p90) REVERT: A 464 TYR cc_start: 0.8383 (m-10) cc_final: 0.8068 (m-80) REVERT: B 163 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6510 (t80) REVERT: B 168 ASP cc_start: 0.7892 (t0) cc_final: 0.7651 (t0) REVERT: B 420 MET cc_start: 0.8271 (tpp) cc_final: 0.8017 (ttm) REVERT: B 472 GLU cc_start: 0.7200 (tp30) cc_final: 0.6919 (tt0) REVERT: C 208 ASP cc_start: 0.7502 (m-30) cc_final: 0.7270 (m-30) REVERT: C 375 MET cc_start: 0.6125 (mtm) cc_final: 0.5807 (mtt) REVERT: C 396 ILE cc_start: 0.8915 (mm) cc_final: 0.8658 (mt) REVERT: D 203 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7531 (t80) REVERT: D 365 MET cc_start: 0.6377 (ttp) cc_final: 0.6105 (ttt) outliers start: 82 outliers final: 46 residues processed: 342 average time/residue: 0.2655 time to fit residues: 144.0446 Evaluate side-chains 296 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 199 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137859 restraints weight = 24211.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140976 restraints weight = 13963.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143074 restraints weight = 9188.274| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18500 Z= 0.210 Angle : 0.761 14.792 25236 Z= 0.384 Chirality : 0.049 0.218 2632 Planarity : 0.006 0.072 3344 Dihedral : 6.409 120.038 2628 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.57 % Favored : 87.39 % Rotamer: Outliers : 4.27 % Allowed : 19.67 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.17), residues: 2180 helix: -1.22 (0.21), residues: 524 sheet: -2.51 (0.28), residues: 352 loop : -2.35 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 227 HIS 0.007 0.001 HIS B 349 PHE 0.027 0.002 PHE A 484 TYR 0.026 0.002 TYR A 198 ARG 0.009 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 359) hydrogen bonds : angle 4.83225 ( 915) covalent geometry : bond 0.00510 (18496) covalent geometry : angle 0.76124 (25236) Misc. bond : bond 0.00078 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 256 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: A 195 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.6987 (mmt180) REVERT: A 262 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7844 (mttp) REVERT: A 356 MET cc_start: 0.5605 (ppp) cc_final: 0.5129 (ppp) REVERT: A 365 MET cc_start: 0.7591 (mtp) cc_final: 0.7093 (mtp) REVERT: A 413 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7308 (t80) REVERT: B 251 CYS cc_start: 0.7936 (m) cc_final: 0.7710 (m) REVERT: B 516 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: C 375 MET cc_start: 0.6298 (mtm) cc_final: 0.5865 (mtt) REVERT: D 203 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7557 (t80) REVERT: D 365 MET cc_start: 0.6537 (ttp) cc_final: 0.6119 (ttm) REVERT: D 393 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7149 (tmm-80) outliers start: 81 outliers final: 47 residues processed: 321 average time/residue: 0.2676 time to fit residues: 135.6313 Evaluate side-chains 278 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 76 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 113 optimal weight: 0.0020 chunk 164 optimal weight: 6.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141822 restraints weight = 23783.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144895 restraints weight = 13807.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146997 restraints weight = 9112.758| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18500 Z= 0.129 Angle : 0.668 14.629 25236 Z= 0.336 Chirality : 0.045 0.215 2632 Planarity : 0.006 0.091 3344 Dihedral : 6.014 118.011 2628 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.32 % Favored : 89.63 % Rotamer: Outliers : 3.27 % Allowed : 20.94 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 2180 helix: -0.98 (0.23), residues: 508 sheet: -2.37 (0.28), residues: 356 loop : -2.06 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 227 HIS 0.006 0.001 HIS B 349 PHE 0.028 0.001 PHE A 484 TYR 0.015 0.001 TYR D 173 ARG 0.005 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 359) hydrogen bonds : angle 4.55678 ( 915) covalent geometry : bond 0.00308 (18496) covalent geometry : angle 0.66772 (25236) Misc. bond : bond 0.00061 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 2.102 Fit side-chains REVERT: A 195 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7026 (mmp-170) REVERT: A 262 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7772 (mttp) REVERT: A 356 MET cc_start: 0.5329 (ppp) cc_final: 0.4710 (ppp) REVERT: A 414 TYR cc_start: 0.8745 (p90) cc_final: 0.8430 (p90) REVERT: B 102 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.6419 (t0) REVERT: B 168 ASP cc_start: 0.8104 (t0) cc_final: 0.7849 (t0) REVERT: B 184 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.4892 (mp0) REVERT: B 203 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 251 CYS cc_start: 0.7883 (m) cc_final: 0.7661 (m) REVERT: B 351 GLU cc_start: 0.6095 (tp30) cc_final: 0.5629 (tp30) REVERT: C 375 MET cc_start: 0.6184 (mtm) cc_final: 0.5978 (mtt) REVERT: D 71 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (tt) REVERT: D 136 ASP cc_start: 0.7788 (t0) cc_final: 0.7480 (t0) REVERT: D 365 MET cc_start: 0.6446 (ttp) cc_final: 0.6132 (ttt) outliers start: 62 outliers final: 40 residues processed: 295 average time/residue: 0.2681 time to fit residues: 125.1881 Evaluate side-chains 269 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 11 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 200 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141830 restraints weight = 23901.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144902 restraints weight = 13819.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146996 restraints weight = 9110.935| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.9302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18500 Z= 0.134 Angle : 0.685 15.678 25236 Z= 0.341 Chirality : 0.046 0.224 2632 Planarity : 0.006 0.097 3344 Dihedral : 5.880 118.463 2628 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.06 % Favored : 88.90 % Rotamer: Outliers : 2.64 % Allowed : 21.99 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.18), residues: 2180 helix: -0.92 (0.22), residues: 516 sheet: -2.28 (0.28), residues: 356 loop : -2.02 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 227 HIS 0.005 0.001 HIS B 349 PHE 0.036 0.001 PHE A 345 TYR 0.015 0.001 TYR D 173 ARG 0.010 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 359) hydrogen bonds : angle 4.50499 ( 915) covalent geometry : bond 0.00319 (18496) covalent geometry : angle 0.68491 (25236) Misc. bond : bond 0.00063 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 1.904 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7364 (p0) cc_final: 0.6196 (t0) REVERT: A 139 MET cc_start: 0.6493 (mmt) cc_final: 0.6213 (mmt) REVERT: A 195 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7083 (mmp-170) REVERT: A 262 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7691 (mttp) REVERT: A 356 MET cc_start: 0.5254 (ppp) cc_final: 0.4644 (ppp) REVERT: A 414 TYR cc_start: 0.8712 (p90) cc_final: 0.8436 (p90) REVERT: B 102 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.6424 (t0) REVERT: B 184 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.4827 (mp0) REVERT: B 203 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6253 (t80) REVERT: B 339 MET cc_start: 0.7462 (tpp) cc_final: 0.6728 (tpp) REVERT: B 351 GLU cc_start: 0.5969 (tp30) cc_final: 0.5413 (tp30) REVERT: B 574 LEU cc_start: 0.6814 (tp) cc_final: 0.6597 (mp) REVERT: C 366 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6189 (t80) REVERT: C 375 MET cc_start: 0.6100 (mtm) cc_final: 0.5654 (mtt) REVERT: D 136 ASP cc_start: 0.7806 (t0) cc_final: 0.7477 (t0) REVERT: D 365 MET cc_start: 0.6528 (ttp) cc_final: 0.6248 (ttt) outliers start: 50 outliers final: 34 residues processed: 280 average time/residue: 0.2665 time to fit residues: 117.5913 Evaluate side-chains 260 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 210 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142196 restraints weight = 23860.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145339 restraints weight = 13990.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147513 restraints weight = 9227.010| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.9650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18500 Z= 0.186 Angle : 0.730 15.514 25236 Z= 0.365 Chirality : 0.048 0.265 2632 Planarity : 0.006 0.099 3344 Dihedral : 6.251 121.865 2628 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.51 % Favored : 88.44 % Rotamer: Outliers : 3.22 % Allowed : 21.62 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.18), residues: 2180 helix: -0.92 (0.22), residues: 500 sheet: -2.13 (0.31), residues: 288 loop : -2.13 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 227 HIS 0.006 0.001 HIS B 349 PHE 0.039 0.002 PHE A 345 TYR 0.019 0.002 TYR A 198 ARG 0.010 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 359) hydrogen bonds : angle 4.65725 ( 915) covalent geometry : bond 0.00453 (18496) covalent geometry : angle 0.73030 (25236) Misc. bond : bond 0.00096 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7330 (p0) cc_final: 0.6188 (t0) REVERT: A 195 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7148 (mmm160) REVERT: A 210 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7464 (t0) REVERT: A 262 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7798 (mttm) REVERT: A 341 GLN cc_start: 0.7445 (tp40) cc_final: 0.7112 (mm110) REVERT: A 356 MET cc_start: 0.5356 (ppp) cc_final: 0.4786 (ppp) REVERT: A 414 TYR cc_start: 0.8701 (p90) cc_final: 0.8442 (p90) REVERT: B 102 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6472 (t0) REVERT: B 184 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.4832 (mp0) REVERT: B 203 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 339 MET cc_start: 0.7499 (tpp) cc_final: 0.6699 (tpp) REVERT: B 362 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5834 (mmp80) REVERT: C 366 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6270 (t80) REVERT: C 375 MET cc_start: 0.6245 (mtm) cc_final: 0.5736 (mtt) REVERT: D 136 ASP cc_start: 0.7876 (t0) cc_final: 0.7585 (t0) REVERT: D 365 MET cc_start: 0.6704 (ttp) cc_final: 0.6370 (ttm) outliers start: 61 outliers final: 41 residues processed: 275 average time/residue: 0.2638 time to fit residues: 113.8060 Evaluate side-chains 261 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 164 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144599 restraints weight = 23804.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147841 restraints weight = 13746.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150039 restraints weight = 9024.901| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.9761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18500 Z= 0.148 Angle : 0.717 15.763 25236 Z= 0.358 Chirality : 0.047 0.259 2632 Planarity : 0.006 0.088 3344 Dihedral : 6.121 121.881 2628 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.33 % Favored : 88.62 % Rotamer: Outliers : 2.64 % Allowed : 22.36 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.18), residues: 2180 helix: -0.86 (0.22), residues: 528 sheet: -2.06 (0.31), residues: 288 loop : -2.07 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 227 HIS 0.006 0.001 HIS B 349 PHE 0.065 0.002 PHE B 484 TYR 0.017 0.001 TYR A 211 ARG 0.008 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 359) hydrogen bonds : angle 4.56628 ( 915) covalent geometry : bond 0.00357 (18496) covalent geometry : angle 0.71660 (25236) Misc. bond : bond 0.00079 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7360 (p0) cc_final: 0.6169 (t0) REVERT: A 139 MET cc_start: 0.6637 (mmt) cc_final: 0.6187 (mmt) REVERT: A 195 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7283 (mmm160) REVERT: A 262 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7761 (mttm) REVERT: A 341 GLN cc_start: 0.7520 (tp40) cc_final: 0.7186 (mm110) REVERT: A 356 MET cc_start: 0.5245 (ppp) cc_final: 0.4713 (ppp) REVERT: A 365 MET cc_start: 0.7706 (mtp) cc_final: 0.7205 (mtp) REVERT: A 414 TYR cc_start: 0.8741 (p90) cc_final: 0.8478 (p90) REVERT: B 63 ASP cc_start: 0.7054 (p0) cc_final: 0.6843 (p0) REVERT: B 102 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.6473 (t0) REVERT: B 184 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.4841 (mp0) REVERT: B 203 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 339 MET cc_start: 0.7451 (tpp) cc_final: 0.6651 (tpp) REVERT: B 341 GLN cc_start: 0.7569 (tp40) cc_final: 0.7294 (tp40) REVERT: B 351 GLU cc_start: 0.6031 (tp30) cc_final: 0.5532 (tp30) REVERT: B 362 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5552 (mmp80) REVERT: C 366 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6073 (t80) REVERT: C 375 MET cc_start: 0.6048 (mtm) cc_final: 0.5681 (mtt) REVERT: D 365 MET cc_start: 0.6636 (ttp) cc_final: 0.6406 (ttt) outliers start: 50 outliers final: 39 residues processed: 266 average time/residue: 0.2581 time to fit residues: 108.2928 Evaluate side-chains 259 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 191 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141585 restraints weight = 23798.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144747 restraints weight = 13884.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.146902 restraints weight = 9192.418| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.9972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18500 Z= 0.190 Angle : 0.746 15.804 25236 Z= 0.373 Chirality : 0.049 0.256 2632 Planarity : 0.006 0.089 3344 Dihedral : 6.276 123.754 2628 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.43 % Favored : 87.52 % Rotamer: Outliers : 2.74 % Allowed : 22.20 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.18), residues: 2180 helix: -0.89 (0.22), residues: 500 sheet: -2.12 (0.31), residues: 288 loop : -2.15 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 227 HIS 0.007 0.001 HIS B 349 PHE 0.051 0.002 PHE B 484 TYR 0.020 0.002 TYR A 198 ARG 0.008 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 359) hydrogen bonds : angle 4.68390 ( 915) covalent geometry : bond 0.00470 (18496) covalent geometry : angle 0.74590 (25236) Misc. bond : bond 0.00100 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.65 seconds wall clock time: 90 minutes 19.60 seconds (5419.60 seconds total)