Starting phenix.real_space_refine on Sat Aug 23 14:56:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bob_16140/08_2025/8bob_16140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bob_16140/08_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_16140/08_2025/8bob_16140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bob_16140/08_2025/8bob_16140.map" model { file = "/net/cci-nas-00/data/ceres_data/8bob_16140/08_2025/8bob_16140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bob_16140/08_2025/8bob_16140.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} 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: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} 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: 2.31, per 1000 atoms: 0.18 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: 0.84 Conformation dependent library (CDL) restraints added in 435.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 1.98 Time building geometry restraints manager: 1.08 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: 0.02 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: 1.260 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG C 19 TYR 0.031 0.002 TYR D 43 PHE 0.020 0.002 PHE A 77 TRP 0.050 0.002 TRP A 14 HIS 0.004 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00914 (13008) covalent geometry : angle 0.87045 (17692) hydrogen bonds : bond 0.16620 ( 672) hydrogen bonds : angle 6.71455 ( 1962) *********************** 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 : 0.425 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: 0.7683 (ptp) REVERT: D 1 MET cc_start: 0.6777 (ttt) cc_final: 0.6501 (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: 0.5501 time to fit residues: 88.6163 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 : 0.323 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 A 336 ASN B 17 GLN B 56 HIS B 75 HIS B 282 GLN B 298 ASN B 336 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063871 restraints weight = 25853.211| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.45 r_work: 0.2835 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13008 Z= 0.147 Angle : 0.608 7.857 17692 Z= 0.310 Chirality : 0.043 0.247 1956 Planarity : 0.004 0.049 2272 Dihedral : 8.727 143.394 1772 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.89 % Allowed : 7.39 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1592 helix: 0.49 (0.17), residues: 890 sheet: -1.12 (0.40), residues: 180 loop : -1.27 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 242 TYR 0.017 0.002 TYR C 254 PHE 0.011 0.001 PHE D 194 TRP 0.017 0.001 TRP A 14 HIS 0.004 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00328 (13008) covalent geometry : angle 0.60849 (17692) hydrogen bonds : bond 0.04080 ( 672) hydrogen bonds : angle 4.92395 ( 1962) *********************** 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 111 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7203 (ttt) cc_final: 0.6529 (mpp) REVERT: C 273 LYS cc_start: 0.9131 (mttt) cc_final: 0.8712 (mtpp) REVERT: C 311 MET cc_start: 0.8854 (mmp) cc_final: 0.8510 (mmm) REVERT: D 1 MET cc_start: 0.7298 (ttt) cc_final: 0.6544 (mpp) REVERT: D 238 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7649 (ttpt) REVERT: D 378 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5873 (mm) outliers start: 25 outliers final: 4 residues processed: 104 average time/residue: 0.5520 time to fit residues: 62.5810 Evaluate side-chains 76 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 259 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 116 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 234 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 = 0.3526 r_free = 0.3526 target = 0.092849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064223 restraints weight = 26023.304| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.44 r_work: 0.2841 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2358 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= 0.123 Angle : 0.551 7.135 17692 Z= 0.278 Chirality : 0.042 0.271 1956 Planarity : 0.004 0.045 2272 Dihedral : 7.403 124.493 1765 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.73 % Allowed : 9.20 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1592 helix: 1.07 (0.18), residues: 884 sheet: -0.92 (0.41), residues: 184 loop : -0.84 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 241 TYR 0.011 0.001 TYR A 82 PHE 0.012 0.001 PHE C 194 TRP 0.011 0.001 TRP A 14 HIS 0.002 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00278 (13008) covalent geometry : angle 0.55063 (17692) hydrogen bonds : bond 0.03317 ( 672) hydrogen bonds : angle 4.51505 ( 1962) *********************** 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 107 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.495 Fit side-chains REVERT: A 390 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7900 (ttt90) REVERT: B 48 GLU cc_start: 0.8729 (tt0) cc_final: 0.8438 (tp30) REVERT: B 390 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7950 (ttt90) REVERT: C 1 MET cc_start: 0.7141 (ttt) cc_final: 0.6419 (mpp) REVERT: C 207 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: C 311 MET cc_start: 0.8745 (mmp) cc_final: 0.8504 (mmm) REVERT: D 1 MET cc_start: 0.7118 (ttt) cc_final: 0.6486 (mpp) REVERT: D 238 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7646 (ttpt) REVERT: D 378 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5654 (mm) outliers start: 23 outliers final: 3 residues processed: 102 average time/residue: 0.5148 time to fit residues: 57.6259 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 234 HIS D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063787 restraints weight = 26081.098| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.45 r_work: 0.2827 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2609 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= 0.133 Angle : 0.558 8.716 17692 Z= 0.278 Chirality : 0.042 0.274 1956 Planarity : 0.003 0.030 2272 Dihedral : 7.163 121.791 1763 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.43 % Allowed : 11.16 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1592 helix: 1.29 (0.18), residues: 886 sheet: -0.69 (0.42), residues: 184 loop : -0.62 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 374 TYR 0.011 0.001 TYR A 98 PHE 0.012 0.001 PHE D 194 TRP 0.009 0.001 TRP A 325 HIS 0.009 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00305 (13008) covalent geometry : angle 0.55802 (17692) hydrogen bonds : bond 0.03279 ( 672) hydrogen bonds : angle 4.42244 ( 1962) *********************** 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 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.401 Fit side-chains REVERT: B 48 GLU cc_start: 0.8775 (tt0) cc_final: 0.8483 (tp30) REVERT: C 1 MET cc_start: 0.7194 (ttt) cc_final: 0.6418 (mpp) REVERT: C 311 MET cc_start: 0.8717 (mmp) cc_final: 0.8342 (mmm) REVERT: C 372 MET cc_start: 0.8921 (tpt) cc_final: 0.8713 (mmm) REVERT: D 1 MET cc_start: 0.7270 (ttt) cc_final: 0.6459 (mpp) REVERT: D 234 HIS cc_start: 0.5137 (m170) cc_final: 0.4797 (m170) REVERT: D 372 MET cc_start: 0.8964 (tpt) cc_final: 0.8751 (mmm) REVERT: D 378 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5537 (pp) outliers start: 19 outliers final: 4 residues processed: 87 average time/residue: 0.5024 time to fit residues: 48.0487 Evaluate side-chains 71 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** C 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062453 restraints weight = 26332.328| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.48 r_work: 0.2800 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13008 Z= 0.173 Angle : 0.577 8.974 17692 Z= 0.288 Chirality : 0.043 0.299 1956 Planarity : 0.004 0.039 2272 Dihedral : 7.312 125.009 1762 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.89 % Allowed : 11.92 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.22), residues: 1592 helix: 1.34 (0.18), residues: 890 sheet: -0.58 (0.42), residues: 184 loop : -0.52 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.012 0.001 TYR A 98 PHE 0.012 0.001 PHE D 194 TRP 0.010 0.001 TRP A 325 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00405 (13008) covalent geometry : angle 0.57707 (17692) hydrogen bonds : bond 0.03545 ( 672) hydrogen bonds : angle 4.44201 ( 1962) *********************** 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 97 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.437 Fit side-chains REVERT: B 48 GLU cc_start: 0.8796 (tt0) cc_final: 0.8531 (tp30) REVERT: C 1 MET cc_start: 0.7260 (ttt) cc_final: 0.6473 (mpp) REVERT: C 372 MET cc_start: 0.8966 (tpt) cc_final: 0.8751 (mmm) REVERT: D 1 MET cc_start: 0.7244 (ttt) cc_final: 0.6481 (mpp) REVERT: D 371 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7899 (pp) REVERT: D 372 MET cc_start: 0.8929 (tpt) cc_final: 0.8723 (tpt) REVERT: D 378 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5911 (pp) outliers start: 25 outliers final: 5 residues processed: 94 average time/residue: 0.4826 time to fit residues: 50.0870 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062463 restraints weight = 26046.561| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.45 r_work: 0.2799 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2761 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= 0.177 Angle : 0.590 9.895 17692 Z= 0.293 Chirality : 0.044 0.358 1956 Planarity : 0.004 0.046 2272 Dihedral : 7.368 126.277 1762 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.28 % Allowed : 12.75 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.22), residues: 1592 helix: 1.37 (0.18), residues: 890 sheet: -0.35 (0.43), residues: 180 loop : -0.55 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.012 0.001 TYR A 98 PHE 0.012 0.001 PHE D 194 TRP 0.010 0.001 TRP A 325 HIS 0.007 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00416 (13008) covalent geometry : angle 0.58981 (17692) hydrogen bonds : bond 0.03528 ( 672) hydrogen bonds : angle 4.44504 ( 1962) *********************** 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 88 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.429 Fit side-chains REVERT: B 48 GLU cc_start: 0.8781 (tt0) cc_final: 0.8502 (tp30) REVERT: C 1 MET cc_start: 0.7266 (ttt) cc_final: 0.6466 (mpp) REVERT: C 311 MET cc_start: 0.8783 (mmm) cc_final: 0.8569 (mmp) REVERT: D 1 MET cc_start: 0.7215 (ttt) cc_final: 0.6483 (mpp) outliers start: 17 outliers final: 8 residues processed: 87 average time/residue: 0.5121 time to fit residues: 48.8569 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 HIS D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064134 restraints weight = 26072.130| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.46 r_work: 0.2839 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13008 Z= 0.115 Angle : 0.551 10.708 17692 Z= 0.272 Chirality : 0.041 0.366 1956 Planarity : 0.003 0.043 2272 Dihedral : 6.997 120.081 1762 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.43 % Allowed : 12.37 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.22), residues: 1592 helix: 1.52 (0.18), residues: 890 sheet: -0.19 (0.43), residues: 180 loop : -0.45 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 390 TYR 0.009 0.001 TYR B 98 PHE 0.012 0.001 PHE D 194 TRP 0.011 0.001 TRP D 382 HIS 0.004 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00258 (13008) covalent geometry : angle 0.55064 (17692) hydrogen bonds : bond 0.02924 ( 672) hydrogen bonds : angle 4.31159 ( 1962) *********************** 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 94 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.347 Fit side-chains REVERT: A 48 GLU cc_start: 0.8734 (tt0) cc_final: 0.8477 (tp30) REVERT: A 148 PHE cc_start: 0.8417 (m-80) cc_final: 0.8120 (p90) REVERT: B 48 GLU cc_start: 0.8692 (tt0) cc_final: 0.8473 (tp30) REVERT: B 148 PHE cc_start: 0.8431 (m-80) cc_final: 0.8161 (p90) REVERT: C 1 MET cc_start: 0.7275 (ttt) cc_final: 0.6448 (mpp) REVERT: C 371 LEU cc_start: 0.8491 (mm) cc_final: 0.7911 (pp) REVERT: C 372 MET cc_start: 0.8858 (tpt) cc_final: 0.8513 (tmm) REVERT: D 1 MET cc_start: 0.7207 (ttt) cc_final: 0.6418 (mpp) REVERT: D 371 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7838 (pp) REVERT: D 372 MET cc_start: 0.8823 (tpt) cc_final: 0.8606 (mmt) outliers start: 19 outliers final: 9 residues processed: 89 average time/residue: 0.5292 time to fit residues: 51.6873 Evaluate side-chains 79 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061611 restraints weight = 26079.623| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.46 r_work: 0.2784 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13008 Z= 0.209 Angle : 0.611 11.395 17692 Z= 0.302 Chirality : 0.043 0.149 1956 Planarity : 0.004 0.040 2272 Dihedral : 7.406 127.381 1762 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.51 % Allowed : 12.90 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.22), residues: 1592 helix: 1.42 (0.18), residues: 884 sheet: -0.20 (0.44), residues: 180 loop : -0.53 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.013 0.002 TYR B 98 PHE 0.012 0.001 PHE D 145 TRP 0.013 0.001 TRP D 382 HIS 0.008 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00491 (13008) covalent geometry : angle 0.61087 (17692) hydrogen bonds : bond 0.03750 ( 672) hydrogen bonds : angle 4.45548 ( 1962) *********************** 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 88 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.328 Fit side-chains REVERT: B 48 GLU cc_start: 0.8808 (tt0) cc_final: 0.8546 (tp30) REVERT: C 1 MET cc_start: 0.7216 (ttt) cc_final: 0.6497 (mpp) REVERT: C 311 MET cc_start: 0.8785 (mmm) cc_final: 0.8544 (mmp) REVERT: C 352 MET cc_start: 0.8903 (tpp) cc_final: 0.8629 (tpp) REVERT: C 391 SER cc_start: 0.8523 (m) cc_final: 0.7993 (t) REVERT: D 1 MET cc_start: 0.7236 (ttt) cc_final: 0.6474 (mpp) REVERT: D 371 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7882 (pp) outliers start: 20 outliers final: 7 residues processed: 81 average time/residue: 0.5008 time to fit residues: 44.6906 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 : 0.348 ------------------------------------------------------------------------------- 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 13 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.092338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063587 restraints weight = 25883.820| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.44 r_work: 0.2827 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13008 Z= 0.125 Angle : 0.568 12.243 17692 Z= 0.277 Chirality : 0.041 0.145 1956 Planarity : 0.004 0.041 2272 Dihedral : 7.094 122.280 1762 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.06 % Allowed : 13.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1592 helix: 1.54 (0.18), residues: 884 sheet: -0.11 (0.44), residues: 180 loop : -0.46 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 374 TYR 0.010 0.001 TYR B 98 PHE 0.011 0.001 PHE D 194 TRP 0.018 0.001 TRP D 382 HIS 0.007 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00287 (13008) covalent geometry : angle 0.56840 (17692) hydrogen bonds : bond 0.03031 ( 672) hydrogen bonds : angle 4.32241 ( 1962) *********************** 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 86 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8737 (tt0) cc_final: 0.8499 (tp30) REVERT: B 48 GLU cc_start: 0.8709 (tt0) cc_final: 0.8481 (tp30) REVERT: C 1 MET cc_start: 0.7229 (ttt) cc_final: 0.6473 (mpp) REVERT: C 311 MET cc_start: 0.8746 (mmm) cc_final: 0.8525 (mmp) REVERT: C 391 SER cc_start: 0.8544 (m) cc_final: 0.8076 (t) REVERT: D 1 MET cc_start: 0.7256 (ttt) cc_final: 0.6457 (mpp) REVERT: D 371 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7876 (pp) REVERT: D 391 SER cc_start: 0.8581 (m) cc_final: 0.7979 (t) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.5253 time to fit residues: 48.4876 Evaluate side-chains 78 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061833 restraints weight = 26296.847| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.46 r_work: 0.2791 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13008 Z= 0.198 Angle : 0.622 12.515 17692 Z= 0.304 Chirality : 0.043 0.148 1956 Planarity : 0.004 0.046 2272 Dihedral : 7.351 126.183 1762 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.83 % Allowed : 13.80 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.22), residues: 1592 helix: 1.43 (0.18), residues: 884 sheet: -0.14 (0.44), residues: 180 loop : -0.51 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 374 TYR 0.012 0.001 TYR B 98 PHE 0.011 0.001 PHE C 194 TRP 0.025 0.001 TRP D 382 HIS 0.009 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00467 (13008) covalent geometry : angle 0.62152 (17692) hydrogen bonds : bond 0.03629 ( 672) hydrogen bonds : angle 4.41814 ( 1962) ********************** 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 81 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8786 (tt0) cc_final: 0.8491 (tp30) REVERT: C 1 MET cc_start: 0.7215 (ttt) cc_final: 0.6445 (mpp) REVERT: C 311 MET cc_start: 0.8785 (mmm) cc_final: 0.8550 (mmp) REVERT: C 391 SER cc_start: 0.8529 (m) cc_final: 0.8017 (t) REVERT: D 1 MET cc_start: 0.7231 (ttt) cc_final: 0.6471 (mpp) REVERT: D 371 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7873 (pp) REVERT: D 372 MET cc_start: 0.8680 (tpt) cc_final: 0.8343 (mmm) REVERT: D 391 SER cc_start: 0.8413 (m) cc_final: 0.7805 (t) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.5067 time to fit residues: 44.6205 Evaluate side-chains 77 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 53 optimal weight: 0.0070 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.062627 restraints weight = 25977.909| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.44 r_work: 0.2807 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13008 Z= 0.159 Angle : 0.588 11.534 17692 Z= 0.289 Chirality : 0.042 0.147 1956 Planarity : 0.004 0.045 2272 Dihedral : 7.252 124.570 1762 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.98 % Allowed : 13.65 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.22), residues: 1592 helix: 1.45 (0.18), residues: 884 sheet: -0.09 (0.44), residues: 180 loop : -0.51 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.011 0.001 TYR A 98 PHE 0.011 0.001 PHE C 194 TRP 0.033 0.001 TRP D 382 HIS 0.009 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00373 (13008) covalent geometry : angle 0.58781 (17692) hydrogen bonds : bond 0.03360 ( 672) hydrogen bonds : angle 4.36700 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.73 seconds wall clock time: 58 minutes 40.21 seconds (3520.21 seconds total)