Starting phenix.real_space_refine on Wed Jun 11 13:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.map" model { file = "/net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bob_16140/06_2025/8bob_16140.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 68 5.16 5 C 8058 2.51 5 N 2214 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3052 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 15, 'TRANS': 370} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3052 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 15, 'TRANS': 370} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3262 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3262 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.82, per 1000 atoms: 0.69 Number of scatterers: 12712 At special positions: 0 Unit cell: (130.503, 126.259, 82.758, 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) S 68 16.00 P 6 15.00 O 2366 8.00 N 2214 7.00 C 8058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 60.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 121 through 131 removed outlier: 4.181A pdb=" N TYR A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.402A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.644A pdb=" N ARG A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.606A pdb=" N LYS A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 121 through 131 removed outlier: 4.182A pdb=" N TYR B 125 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.097A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 249 through 262 removed outlier: 3.643A pdb=" N ARG B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 284 through 310 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.606A pdb=" N LYS B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 19 through 28 removed outlier: 3.792A pdb=" N LYS C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 32 removed outlier: 3.695A pdb=" N PHE C 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 32' Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 87 Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.922A pdb=" N GLU C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.632A pdb=" N LEU C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.734A pdb=" N LEU C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.527A pdb=" N ALA C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 204 through 215 removed outlier: 3.611A pdb=" N VAL C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 231 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.867A pdb=" N TRP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 369 through 387 removed outlier: 6.455A pdb=" N TRP C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 406 through 417 removed outlier: 4.886A pdb=" N ALA C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 19 through 28 removed outlier: 3.593A pdb=" N LEU D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 32 removed outlier: 3.696A pdb=" N PHE D 32 " --> pdb=" O ALA D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 32' Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 87 Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.928A pdb=" N GLU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.632A pdb=" N LEU D 132 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.735A pdb=" N LEU D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.527A pdb=" N ALA D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.654A pdb=" N VAL D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 231 Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 281 through 289 Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.867A pdb=" N TRP D 334 " --> pdb=" O GLN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 356 through 368 Processing helix chain 'D' and resid 369 through 387 removed outlier: 6.454A pdb=" N TRP D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 3.682A pdb=" N LYS D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.759A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.311A pdb=" N LEU A 31 " --> pdb=" O ALA A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.695A pdb=" N LYS A 164 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 199 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET A 166 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP A 201 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 168 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY A 113 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU A 167 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 115 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N CYS A 169 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS A 117 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 114 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 138 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 116 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 327 removed outlier: 3.819A pdb=" N MET A 351 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.310A pdb=" N LEU B 31 " --> pdb=" O ALA B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.696A pdb=" N LYS B 164 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE B 199 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET B 166 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP B 201 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 168 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 113 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU B 167 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 115 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N CYS B 169 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS B 117 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL B 114 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL B 138 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 116 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA8, first strand: chain 'B' and resid 323 through 327 removed outlier: 3.820A pdb=" N MET B 351 " --> pdb=" O ARG B 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 63 removed outlier: 6.618A pdb=" N GLY C 60 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP C 128 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR C 62 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 310 Processing sheet with id=AB2, first strand: chain 'D' and resid 59 through 63 removed outlier: 6.617A pdb=" N GLY D 60 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP D 128 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR D 62 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 310 672 hydrogen bonds defined for protein. 1962 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: 4.66 Time building geometry restraints manager: 3.80 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: 2904 1.33 - 1.45: 2849 1.45 - 1.57: 7139 1.57 - 1.69: 8 1.69 - 1.81: 108 Bond restraints: 13008 Sorted by residual: bond pdb=" N ILE B 215 " pdb=" CA ILE B 215 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.01e-02 9.80e+03 1.01e+01 bond pdb=" N ILE C 410 " pdb=" CA ILE C 410 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N VAL A 220 " pdb=" CA VAL A 220 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.17e+00 bond pdb=" N ARG B 222 " pdb=" CA ARG B 222 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.26e-02 6.30e+03 8.80e+00 bond pdb=" N VAL B 220 " pdb=" CA VAL B 220 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.72e+00 ... (remaining 13003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16928 2.02 - 4.04: 682 4.04 - 6.05: 71 6.05 - 8.07: 9 8.07 - 10.09: 2 Bond angle restraints: 17692 Sorted by residual: angle pdb=" CA ALA C 409 " pdb=" C ALA C 409 " pdb=" O ALA C 409 " ideal model delta sigma weight residual 120.55 115.67 4.88 1.06e+00 8.90e-01 2.12e+01 angle pdb=" N PRO D 406 " pdb=" CA PRO D 406 " pdb=" C PRO D 406 " ideal model delta sigma weight residual 113.53 107.60 5.93 1.39e+00 5.18e-01 1.82e+01 angle pdb=" N ALA C 408 " pdb=" CA ALA C 408 " pdb=" C ALA C 408 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N ILE D 414 " pdb=" CA ILE D 414 " pdb=" C ILE D 414 " ideal model delta sigma weight residual 110.62 106.60 4.02 1.02e+00 9.61e-01 1.55e+01 angle pdb=" N ILE C 114 " pdb=" CA ILE C 114 " pdb=" C ILE C 114 " ideal model delta sigma weight residual 110.23 106.22 4.01 1.04e+00 9.25e-01 1.49e+01 ... (remaining 17687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 7540 35.21 - 70.41: 154 70.41 - 105.62: 8 105.62 - 140.83: 4 140.83 - 176.04: 2 Dihedral angle restraints: 7708 sinusoidal: 3036 harmonic: 4672 Sorted by residual: dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 123.96 176.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 124.00 175.99 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 57.75 -117.75 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 7705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1437 0.056 - 0.113: 437 0.113 - 0.169: 59 0.169 - 0.225: 14 0.225 - 0.281: 9 Chirality restraints: 1956 Sorted by residual: chirality pdb=" CA TYR C 43 " pdb=" N TYR C 43 " pdb=" C TYR C 43 " pdb=" CB TYR C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR D 43 " pdb=" N TYR D 43 " pdb=" C TYR D 43 " pdb=" CB TYR D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE C 114 " pdb=" N ILE C 114 " pdb=" C ILE C 114 " pdb=" CB ILE C 114 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1953 not shown) Planarity restraints: 2272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 14 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP A 14 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 14 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 14 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 14 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 14 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 14 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 14 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 14 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 14 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 14 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.11e+00 pdb=" CG TRP B 14 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 14 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 14 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 14 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 14 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 14 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 14 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 14 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 14 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 409 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C ALA C 409 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA C 409 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE C 410 " 0.017 2.00e-02 2.50e+03 ... (remaining 2269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1980 2.75 - 3.28: 12819 3.28 - 3.82: 21594 3.82 - 4.36: 26076 4.36 - 4.90: 43440 Nonbonded interactions: 105909 Sorted by model distance: nonbonded pdb=" OG SER D 8 " pdb=" O MET D 311 " model vdw 2.208 3.040 nonbonded pdb=" OG SER C 8 " pdb=" O MET C 311 " model vdw 2.208 3.040 nonbonded pdb=" NH1 ARG C 242 " pdb=" OE2 GLU C 258 " model vdw 2.210 3.120 nonbonded pdb=" NH1 ARG D 242 " pdb=" OE2 GLU D 258 " model vdw 2.210 3.120 nonbonded pdb=" OE1 GLU D 291 " pdb=" N ASN D 293 " model vdw 2.215 3.120 ... (remaining 105904 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.290 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.009 0.074 13008 Z= 0.449 Angle : 0.870 10.090 17692 Z= 0.544 Chirality : 0.056 0.281 1956 Planarity : 0.004 0.046 2272 Dihedral : 15.310 176.037 4680 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.21 % Favored : 95.48 % Rotamer: Outliers : 3.17 % Allowed : 4.75 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.19), residues: 1592 helix: -0.78 (0.16), residues: 860 sheet: -1.78 (0.37), residues: 194 loop : -1.74 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 14 HIS 0.004 0.001 HIS D 344 PHE 0.020 0.002 PHE A 77 TYR 0.031 0.002 TYR D 43 ARG 0.005 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.16620 ( 672) hydrogen bonds : angle 6.71455 ( 1962) covalent geometry : bond 0.00914 (13008) covalent geometry : angle 0.87045 (17692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 351 MET cc_start: 0.8384 (tpp) cc_final: 0.8115 (tpt) REVERT: B 351 MET cc_start: 0.8486 (tpp) cc_final: 0.8227 (tpt) REVERT: C 1 MET cc_start: 0.6596 (ttt) cc_final: 0.6299 (mpp) REVERT: C 273 LYS cc_start: 0.9123 (mttt) cc_final: 0.8718 (mtpp) REVERT: C 280 MET cc_start: 0.7896 (mtm) cc_final: 0.7684 (ptp) REVERT: D 1 MET cc_start: 0.6777 (ttt) cc_final: 0.6500 (mpp) REVERT: D 280 MET cc_start: 0.7843 (mtm) cc_final: 0.7486 (ptp) outliers start: 42 outliers final: 6 residues processed: 148 average time/residue: 1.3054 time to fit residues: 210.3863 Evaluate side-chains 75 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 56 HIS A 75 HIS A 219 ASN A 282 GLN A 298 ASN B 17 GLN B 56 HIS B 75 HIS B 282 GLN B 298 ASN C 30 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS C 262 ASN C 269 HIS C 405 ASN D 30 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 262 ASN D 269 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065407 restraints weight = 25839.075| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.42 r_work: 0.2860 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13008 Z= 0.131 Angle : 0.591 7.774 17692 Z= 0.301 Chirality : 0.042 0.237 1956 Planarity : 0.004 0.054 2272 Dihedral : 8.463 141.011 1772 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.11 % Allowed : 7.09 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1592 helix: 0.58 (0.17), residues: 888 sheet: -1.12 (0.40), residues: 180 loop : -1.21 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 14 HIS 0.005 0.001 HIS C 237 PHE 0.011 0.001 PHE D 194 TYR 0.019 0.002 TYR C 254 ARG 0.014 0.001 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 672) hydrogen bonds : angle 4.82238 ( 1962) covalent geometry : bond 0.00282 (13008) covalent geometry : angle 0.59096 (17692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.517 Fit side-chains REVERT: C 1 MET cc_start: 0.7169 (ttt) cc_final: 0.6517 (mpp) REVERT: C 13 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6683 (pp) REVERT: C 280 MET cc_start: 0.8568 (mtm) cc_final: 0.8230 (ptm) REVERT: C 311 MET cc_start: 0.8795 (mmp) cc_final: 0.8441 (mmm) REVERT: C 343 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8645 (tt) REVERT: D 1 MET cc_start: 0.7271 (ttt) cc_final: 0.6545 (mpp) REVERT: D 238 LYS cc_start: 0.7973 (ttpt) cc_final: 0.6492 (ttpm) outliers start: 28 outliers final: 7 residues processed: 107 average time/residue: 1.2273 time to fit residues: 144.3635 Evaluate side-chains 78 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 83 GLN ** 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 = 0.3499 r_free = 0.3499 target = 0.091291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062263 restraints weight = 26250.666| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.46 r_work: 0.2799 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13008 Z= 0.181 Angle : 0.592 7.315 17692 Z= 0.299 Chirality : 0.043 0.256 1956 Planarity : 0.004 0.049 2272 Dihedral : 7.679 127.595 1765 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.19 % Allowed : 9.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1592 helix: 0.99 (0.18), residues: 880 sheet: -0.89 (0.41), residues: 184 loop : -0.89 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 14 HIS 0.003 0.001 HIS D 15 PHE 0.012 0.001 PHE C 194 TYR 0.015 0.002 TYR B 98 ARG 0.007 0.001 ARG D 374 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 672) hydrogen bonds : angle 4.61836 ( 1962) covalent geometry : bond 0.00420 (13008) covalent geometry : angle 0.59194 (17692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.385 Fit side-chains REVERT: A 148 PHE cc_start: 0.8603 (m-80) cc_final: 0.8395 (m-80) REVERT: A 390 ARG cc_start: 0.8165 (tpt-90) cc_final: 0.7961 (ttt90) REVERT: B 390 ARG cc_start: 0.8143 (tpt-90) cc_final: 0.7937 (ttt90) REVERT: C 1 MET cc_start: 0.7141 (ttt) cc_final: 0.6426 (mpp) REVERT: C 13 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6743 (pp) REVERT: C 207 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: C 273 LYS cc_start: 0.9127 (mttt) cc_final: 0.8703 (mtpp) REVERT: C 311 MET cc_start: 0.8768 (mmp) cc_final: 0.8328 (mmm) REVERT: D 1 MET cc_start: 0.7252 (ttt) cc_final: 0.6489 (mpp) outliers start: 29 outliers final: 5 residues processed: 99 average time/residue: 1.2126 time to fit residues: 132.2806 Evaluate side-chains 73 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063696 restraints weight = 25957.442| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.45 r_work: 0.2829 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13008 Z= 0.128 Angle : 0.551 8.703 17692 Z= 0.275 Chirality : 0.042 0.289 1956 Planarity : 0.003 0.030 2272 Dihedral : 7.198 122.085 1763 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.89 % Allowed : 11.24 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1592 helix: 1.26 (0.18), residues: 886 sheet: -0.62 (0.42), residues: 182 loop : -0.68 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.010 0.001 HIS D 380 PHE 0.012 0.001 PHE D 194 TYR 0.010 0.001 TYR A 98 ARG 0.007 0.000 ARG D 374 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 672) hydrogen bonds : angle 4.42859 ( 1962) covalent geometry : bond 0.00292 (13008) covalent geometry : angle 0.55099 (17692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.503 Fit side-chains REVERT: A 48 GLU cc_start: 0.8767 (tt0) cc_final: 0.8520 (tp30) REVERT: A 148 PHE cc_start: 0.8572 (m-80) cc_final: 0.8371 (m-80) REVERT: B 48 GLU cc_start: 0.8771 (tt0) cc_final: 0.8490 (tp30) REVERT: C 1 MET cc_start: 0.7214 (ttt) cc_final: 0.6415 (mpp) REVERT: C 311 MET cc_start: 0.8728 (mmp) cc_final: 0.8375 (mmm) REVERT: D 1 MET cc_start: 0.7221 (ttt) cc_final: 0.6448 (mpp) REVERT: D 234 HIS cc_start: 0.5311 (m170) cc_final: 0.5057 (m170) outliers start: 25 outliers final: 4 residues processed: 96 average time/residue: 1.1064 time to fit residues: 118.0869 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS C 380 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064651 restraints weight = 25968.840| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.46 r_work: 0.2850 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13008 Z= 0.104 Angle : 0.532 9.233 17692 Z= 0.262 Chirality : 0.040 0.141 1956 Planarity : 0.004 0.048 2272 Dihedral : 6.813 115.543 1762 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.51 % Allowed : 11.92 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1592 helix: 1.48 (0.18), residues: 888 sheet: -0.17 (0.43), residues: 176 loop : -0.55 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.006 0.001 HIS C 380 PHE 0.012 0.001 PHE D 194 TYR 0.008 0.001 TYR A 98 ARG 0.008 0.000 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 672) hydrogen bonds : angle 4.29247 ( 1962) covalent geometry : bond 0.00231 (13008) covalent geometry : angle 0.53166 (17692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.424 Fit side-chains REVERT: A 48 GLU cc_start: 0.8751 (tt0) cc_final: 0.8471 (tp30) REVERT: B 48 GLU cc_start: 0.8745 (tt0) cc_final: 0.8516 (tp30) REVERT: C 1 MET cc_start: 0.7204 (ttt) cc_final: 0.6435 (mpp) REVERT: C 311 MET cc_start: 0.8709 (mmp) cc_final: 0.8274 (mmm) REVERT: C 371 LEU cc_start: 0.8379 (mm) cc_final: 0.7838 (pp) REVERT: C 372 MET cc_start: 0.8868 (tpt) cc_final: 0.8624 (mmm) REVERT: C 378 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6115 (pp) REVERT: D 1 MET cc_start: 0.7275 (ttt) cc_final: 0.6452 (mpp) REVERT: D 371 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7897 (pp) REVERT: D 372 MET cc_start: 0.8866 (tpt) cc_final: 0.8578 (mmm) outliers start: 20 outliers final: 5 residues processed: 98 average time/residue: 1.2157 time to fit residues: 131.1801 Evaluate side-chains 78 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 147 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.064452 restraints weight = 26156.282| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.48 r_work: 0.2846 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13008 Z= 0.109 Angle : 0.542 9.849 17692 Z= 0.264 Chirality : 0.041 0.164 1956 Planarity : 0.003 0.030 2272 Dihedral : 6.698 112.621 1762 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.28 % Allowed : 13.20 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1592 helix: 1.57 (0.18), residues: 890 sheet: -0.09 (0.43), residues: 176 loop : -0.44 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 325 HIS 0.002 0.000 HIS D 363 PHE 0.011 0.001 PHE C 194 TYR 0.009 0.001 TYR B 98 ARG 0.005 0.000 ARG D 374 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 672) hydrogen bonds : angle 4.25995 ( 1962) covalent geometry : bond 0.00246 (13008) covalent geometry : angle 0.54220 (17692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.509 Fit side-chains REVERT: A 48 GLU cc_start: 0.8763 (tt0) cc_final: 0.8484 (tp30) REVERT: B 48 GLU cc_start: 0.8750 (tt0) cc_final: 0.8498 (tp30) REVERT: C 1 MET cc_start: 0.7200 (ttt) cc_final: 0.6453 (mpp) REVERT: C 311 MET cc_start: 0.8673 (mmp) cc_final: 0.8214 (mmm) REVERT: C 371 LEU cc_start: 0.8342 (mm) cc_final: 0.7811 (pp) REVERT: C 372 MET cc_start: 0.8904 (tpt) cc_final: 0.8616 (mmm) REVERT: C 378 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6222 (pp) REVERT: D 1 MET cc_start: 0.7262 (ttt) cc_final: 0.6486 (mpp) outliers start: 17 outliers final: 7 residues processed: 89 average time/residue: 1.2793 time to fit residues: 126.6042 Evaluate side-chains 75 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 380 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061950 restraints weight = 26041.695| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.44 r_work: 0.2788 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13008 Z= 0.204 Angle : 0.601 10.906 17692 Z= 0.296 Chirality : 0.043 0.158 1956 Planarity : 0.004 0.036 2272 Dihedral : 7.242 123.884 1762 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.36 % Allowed : 13.95 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1592 helix: 1.47 (0.18), residues: 882 sheet: -0.22 (0.43), residues: 178 loop : -0.50 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 382 HIS 0.004 0.001 HIS D 363 PHE 0.012 0.001 PHE D 145 TYR 0.013 0.002 TYR B 98 ARG 0.006 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 672) hydrogen bonds : angle 4.42510 ( 1962) covalent geometry : bond 0.00484 (13008) covalent geometry : angle 0.60095 (17692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.476 Fit side-chains REVERT: A 390 ARG cc_start: 0.8215 (tpt-90) cc_final: 0.7919 (ttt90) REVERT: B 48 GLU cc_start: 0.8772 (tt0) cc_final: 0.8529 (tp30) REVERT: C 1 MET cc_start: 0.7259 (ttt) cc_final: 0.6486 (mpp) REVERT: C 311 MET cc_start: 0.8770 (mmp) cc_final: 0.8434 (mmm) REVERT: C 378 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6216 (pp) REVERT: C 391 SER cc_start: 0.8488 (m) cc_final: 0.7976 (t) REVERT: D 1 MET cc_start: 0.7204 (ttt) cc_final: 0.6471 (mpp) outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 1.2074 time to fit residues: 107.8464 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063994 restraints weight = 25968.446| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.46 r_work: 0.2835 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13008 Z= 0.115 Angle : 0.540 11.557 17692 Z= 0.265 Chirality : 0.041 0.157 1956 Planarity : 0.003 0.031 2272 Dihedral : 6.965 119.952 1762 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.90 % Allowed : 14.18 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1592 helix: 1.56 (0.18), residues: 890 sheet: -0.09 (0.43), residues: 178 loop : -0.43 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 382 HIS 0.004 0.001 HIS D 380 PHE 0.011 0.001 PHE D 194 TYR 0.009 0.001 TYR A 98 ARG 0.006 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 672) hydrogen bonds : angle 4.28727 ( 1962) covalent geometry : bond 0.00263 (13008) covalent geometry : angle 0.54023 (17692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.348 Fit side-chains REVERT: A 48 GLU cc_start: 0.8734 (tt0) cc_final: 0.8493 (tp30) REVERT: B 48 GLU cc_start: 0.8714 (tt0) cc_final: 0.8477 (tp30) REVERT: C 1 MET cc_start: 0.7272 (ttt) cc_final: 0.6456 (mpp) REVERT: C 311 MET cc_start: 0.8699 (mmp) cc_final: 0.8401 (mmm) REVERT: C 378 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6281 (pp) REVERT: C 391 SER cc_start: 0.8530 (m) cc_final: 0.8012 (t) REVERT: D 1 MET cc_start: 0.7235 (ttt) cc_final: 0.6444 (mpp) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 1.2715 time to fit residues: 110.5418 Evaluate side-chains 72 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064372 restraints weight = 25906.059| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.48 r_work: 0.2845 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13008 Z= 0.107 Angle : 0.542 12.251 17692 Z= 0.265 Chirality : 0.040 0.155 1956 Planarity : 0.003 0.036 2272 Dihedral : 6.760 114.705 1762 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.90 % Allowed : 14.25 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1592 helix: 1.64 (0.18), residues: 886 sheet: 0.10 (0.44), residues: 176 loop : -0.38 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 382 HIS 0.004 0.001 HIS D 237 PHE 0.011 0.001 PHE D 194 TYR 0.009 0.001 TYR A 98 ARG 0.007 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 672) hydrogen bonds : angle 4.22327 ( 1962) covalent geometry : bond 0.00242 (13008) covalent geometry : angle 0.54195 (17692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.343 Fit side-chains REVERT: A 48 GLU cc_start: 0.8733 (tt0) cc_final: 0.8447 (tp30) REVERT: A 351 MET cc_start: 0.8927 (tpt) cc_final: 0.8605 (tpp) REVERT: B 48 GLU cc_start: 0.8727 (tt0) cc_final: 0.8472 (tp30) REVERT: B 351 MET cc_start: 0.8957 (tpt) cc_final: 0.8623 (tpp) REVERT: C 1 MET cc_start: 0.7233 (ttt) cc_final: 0.6446 (mpp) REVERT: C 250 HIS cc_start: 0.8664 (m90) cc_final: 0.8185 (m-70) REVERT: C 311 MET cc_start: 0.8687 (mmp) cc_final: 0.8369 (mmm) REVERT: C 391 SER cc_start: 0.8493 (m) cc_final: 0.7961 (t) REVERT: D 1 MET cc_start: 0.7276 (ttt) cc_final: 0.6425 (mpp) REVERT: D 234 HIS cc_start: 0.5014 (m170) cc_final: 0.4666 (m170) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 1.2844 time to fit residues: 114.4826 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 143 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.063782 restraints weight = 25909.787| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.46 r_work: 0.2831 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13008 Z= 0.127 Angle : 0.549 12.563 17692 Z= 0.270 Chirality : 0.041 0.149 1956 Planarity : 0.003 0.036 2272 Dihedral : 6.777 114.418 1762 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.83 % Allowed : 14.56 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1592 helix: 1.63 (0.18), residues: 880 sheet: 0.01 (0.44), residues: 178 loop : -0.37 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 382 HIS 0.006 0.001 HIS D 380 PHE 0.013 0.001 PHE B 148 TYR 0.010 0.001 TYR A 98 ARG 0.007 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 672) hydrogen bonds : angle 4.25069 ( 1962) covalent geometry : bond 0.00295 (13008) covalent geometry : angle 0.54922 (17692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.372 Fit side-chains REVERT: A 48 GLU cc_start: 0.8755 (tt0) cc_final: 0.8507 (tp30) REVERT: A 351 MET cc_start: 0.8948 (tpt) cc_final: 0.8745 (tpp) REVERT: B 48 GLU cc_start: 0.8716 (tt0) cc_final: 0.8453 (tp30) REVERT: B 351 MET cc_start: 0.8985 (tpt) cc_final: 0.8681 (tpp) REVERT: C 1 MET cc_start: 0.7243 (ttt) cc_final: 0.6471 (mpp) REVERT: C 250 HIS cc_start: 0.8668 (m90) cc_final: 0.8188 (m-70) REVERT: C 311 MET cc_start: 0.8665 (mmp) cc_final: 0.8351 (mmm) REVERT: C 391 SER cc_start: 0.8545 (m) cc_final: 0.8092 (t) REVERT: D 1 MET cc_start: 0.7233 (ttt) cc_final: 0.6440 (mpp) REVERT: D 234 HIS cc_start: 0.5182 (m170) cc_final: 0.4823 (m170) REVERT: D 391 SER cc_start: 0.8496 (m) cc_final: 0.7924 (t) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 1.2949 time to fit residues: 108.2667 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064172 restraints weight = 25892.105| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.47 r_work: 0.2841 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13008 Z= 0.117 Angle : 0.545 12.243 17692 Z= 0.266 Chirality : 0.041 0.146 1956 Planarity : 0.003 0.035 2272 Dihedral : 6.681 112.465 1762 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.68 % Allowed : 14.93 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1592 helix: 1.67 (0.18), residues: 880 sheet: 0.09 (0.44), residues: 178 loop : -0.37 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 382 HIS 0.011 0.001 HIS D 380 PHE 0.012 0.001 PHE B 148 TYR 0.009 0.001 TYR B 98 ARG 0.007 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 672) hydrogen bonds : angle 4.20061 ( 1962) covalent geometry : bond 0.00269 (13008) covalent geometry : angle 0.54451 (17692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8195.13 seconds wall clock time: 140 minutes 33.11 seconds (8433.11 seconds total)