Starting phenix.real_space_refine on Mon Dec 30 09:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bob_16140/12_2024/8bob_16140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bob_16140/12_2024/8bob_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_16140/12_2024/8bob_16140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bob_16140/12_2024/8bob_16140.map" model { file = "/net/cci-nas-00/data/ceres_data/8bob_16140/12_2024/8bob_16140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bob_16140/12_2024/8bob_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.93, per 1000 atoms: 0.62 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 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: 1.51 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: 4.33 Time building geometry restraints manager: 3.95 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: 0.00 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: 1.080 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.520 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.500 ------------------------------------------------------------------------------- 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= 0.596 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 *********************** 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 : 1.611 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: 1.3502 time to fit residues: 217.1820 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 : 1.560 ------------------------------------------------------------------------------- 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 A 336 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13008 Z= 0.183 Angle : 0.595 7.919 17692 Z= 0.303 Chirality : 0.042 0.242 1956 Planarity : 0.005 0.062 2272 Dihedral : 8.535 141.912 1772 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.11 % Allowed : 7.24 % Favored : 90.65 % 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: -0.36 (0.21), residues: 1592 helix: 0.59 (0.17), residues: 884 sheet: -1.12 (0.40), residues: 180 loop : -1.19 (0.25), residues: 528 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 0.001 TYR C 254 ARG 0.009 0.001 ARG D 242 *********************** 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 115 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.529 Fit side-chains REVERT: C 280 MET cc_start: 0.7920 (mtm) cc_final: 0.7624 (ptm) REVERT: C 311 MET cc_start: 0.8310 (mmp) cc_final: 0.8098 (mmm) REVERT: D 238 LYS cc_start: 0.6867 (ttpt) cc_final: 0.5350 (ttpt) REVERT: D 378 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4633 (mm) outliers start: 28 outliers final: 6 residues processed: 106 average time/residue: 1.2837 time to fit residues: 149.8952 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 : 1.543 ------------------------------------------------------------------------------- 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 249 SER Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 378 LEU 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 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 0.0010 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13008 Z= 0.152 Angle : 0.541 6.948 17692 Z= 0.271 Chirality : 0.041 0.252 1956 Planarity : 0.004 0.039 2272 Dihedral : 7.298 122.732 1765 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.51 % Allowed : 9.28 % Favored : 89.22 % 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: 0.30 (0.21), residues: 1592 helix: 1.07 (0.18), residues: 886 sheet: -0.78 (0.41), residues: 180 loop : -0.83 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS D 15 PHE 0.012 0.001 PHE C 194 TYR 0.011 0.001 TYR A 82 ARG 0.008 0.000 ARG C 241 *********************** 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 103 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.618 Fit side-chains REVERT: A 390 ARG cc_start: 0.7560 (tpt-90) cc_final: 0.7348 (ttt90) REVERT: D 392 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6912 (tm) outliers start: 20 outliers final: 2 residues processed: 97 average time/residue: 1.2296 time to fit residues: 131.8422 Evaluate side-chains 70 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13008 Z= 0.231 Angle : 0.576 8.834 17692 Z= 0.285 Chirality : 0.042 0.245 1956 Planarity : 0.003 0.032 2272 Dihedral : 7.303 123.474 1763 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.66 % Allowed : 11.46 % 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: 0.58 (0.22), residues: 1592 helix: 1.27 (0.18), residues: 886 sheet: -0.64 (0.42), residues: 182 loop : -0.66 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 14 HIS 0.003 0.001 HIS C 363 PHE 0.012 0.001 PHE D 194 TYR 0.012 0.001 TYR A 82 ARG 0.006 0.000 ARG B 390 *********************** 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 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.612 Fit side-chains REVERT: A 36 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8772 (m) REVERT: C 371 LEU cc_start: 0.7912 (mm) cc_final: 0.7451 (pp) REVERT: D 392 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6953 (tm) outliers start: 22 outliers final: 3 residues processed: 92 average time/residue: 1.1725 time to fit residues: 119.7539 Evaluate side-chains 73 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 249 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13008 Z= 0.408 Angle : 0.655 9.559 17692 Z= 0.327 Chirality : 0.046 0.302 1956 Planarity : 0.004 0.044 2272 Dihedral : 7.808 133.337 1763 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 1.96 % Allowed : 12.44 % 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 (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: 0.48 (0.21), residues: 1592 helix: 1.12 (0.18), residues: 882 sheet: -0.44 (0.42), residues: 180 loop : -0.66 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 325 HIS 0.004 0.001 HIS C 15 PHE 0.013 0.002 PHE D 145 TYR 0.015 0.002 TYR A 98 ARG 0.008 0.001 ARG D 374 *********************** 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 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 1.540 Fit side-chains REVERT: C 273 LYS cc_start: 0.9102 (mttt) cc_final: 0.8643 (mtpp) REVERT: D 392 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6935 (tm) outliers start: 26 outliers final: 5 residues processed: 89 average time/residue: 1.1804 time to fit residues: 117.2276 Evaluate side-chains 72 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13008 Z= 0.158 Angle : 0.560 9.807 17692 Z= 0.276 Chirality : 0.042 0.363 1956 Planarity : 0.003 0.030 2272 Dihedral : 7.078 120.935 1762 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.06 % Allowed : 13.73 % Favored : 85.22 % 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: 0.85 (0.22), residues: 1592 helix: 1.43 (0.18), residues: 888 sheet: -0.32 (0.43), residues: 180 loop : -0.50 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 325 HIS 0.003 0.000 HIS D 237 PHE 0.012 0.001 PHE D 194 TYR 0.008 0.001 TYR B 98 ARG 0.006 0.000 ARG D 374 *********************** 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 87 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.524 Fit side-chains REVERT: C 371 LEU cc_start: 0.7770 (mm) cc_final: 0.7532 (pp) REVERT: C 391 SER cc_start: 0.7957 (m) cc_final: 0.7666 (t) outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 1.2519 time to fit residues: 116.7064 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 : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET 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 59 ILE 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 149 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3099 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= 0.165 Angle : 0.551 10.781 17692 Z= 0.270 Chirality : 0.041 0.186 1956 Planarity : 0.003 0.040 2272 Dihedral : 6.849 116.678 1762 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.28 % Allowed : 13.50 % Favored : 85.22 % 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: 1.03 (0.22), residues: 1592 helix: 1.54 (0.18), residues: 890 sheet: -0.13 (0.43), residues: 178 loop : -0.42 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 382 HIS 0.008 0.001 HIS D 234 PHE 0.011 0.001 PHE C 194 TYR 0.009 0.001 TYR B 98 ARG 0.008 0.000 ARG B 390 *********************** 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 85 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.628 Fit side-chains REVERT: C 259 VAL cc_start: 0.8578 (t) cc_final: 0.8328 (t) REVERT: C 391 SER cc_start: 0.7944 (m) cc_final: 0.7657 (t) REVERT: D 391 SER cc_start: 0.8080 (m) cc_final: 0.7724 (t) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 1.1830 time to fit residues: 106.3336 Evaluate side-chains 76 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 313 ASP 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 95 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13008 Z= 0.143 Angle : 0.543 11.453 17692 Z= 0.264 Chirality : 0.040 0.144 1956 Planarity : 0.003 0.038 2272 Dihedral : 6.626 111.072 1762 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.13 % Allowed : 13.57 % Favored : 85.29 % 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: 1.64 (0.18), residues: 890 sheet: 0.08 (0.44), residues: 176 loop : -0.37 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 382 HIS 0.004 0.001 HIS D 234 PHE 0.011 0.001 PHE C 194 TYR 0.008 0.001 TYR B 98 ARG 0.009 0.000 ARG B 390 *********************** 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 87 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.579 Fit side-chains REVERT: C 391 SER cc_start: 0.7961 (m) cc_final: 0.7654 (t) REVERT: D 391 SER cc_start: 0.8147 (m) cc_final: 0.7708 (t) outliers start: 15 outliers final: 6 residues processed: 83 average time/residue: 1.2941 time to fit residues: 118.5892 Evaluate side-chains 70 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 140 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13008 Z= 0.250 Angle : 0.589 12.094 17692 Z= 0.288 Chirality : 0.042 0.152 1956 Planarity : 0.003 0.038 2272 Dihedral : 6.910 116.524 1762 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.83 % Allowed : 14.63 % Favored : 84.54 % 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: 1.11 (0.22), residues: 1592 helix: 1.61 (0.18), residues: 882 sheet: -0.05 (0.44), residues: 178 loop : -0.39 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 382 HIS 0.004 0.001 HIS D 234 PHE 0.011 0.001 PHE B 148 TYR 0.011 0.001 TYR B 98 ARG 0.007 0.000 ARG B 390 *********************** 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 76 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.602 Fit side-chains REVERT: C 259 VAL cc_start: 0.8637 (t) cc_final: 0.8390 (t) REVERT: C 391 SER cc_start: 0.7948 (m) cc_final: 0.7615 (t) REVERT: D 391 SER cc_start: 0.7987 (m) cc_final: 0.7704 (t) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 1.2326 time to fit residues: 100.0158 Evaluate side-chains 69 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 151 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 0.0370 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13008 Z= 0.207 Angle : 0.586 12.538 17692 Z= 0.284 Chirality : 0.041 0.159 1956 Planarity : 0.003 0.030 2272 Dihedral : 6.941 119.373 1762 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.53 % Allowed : 15.08 % 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: 1.07 (0.22), residues: 1592 helix: 1.56 (0.18), residues: 884 sheet: -0.01 (0.44), residues: 178 loop : -0.40 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 382 HIS 0.004 0.001 HIS D 234 PHE 0.013 0.001 PHE A 148 TYR 0.010 0.001 TYR A 98 ARG 0.005 0.000 ARG D 374 ********************** 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 75 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.481 Fit side-chains REVERT: C 259 VAL cc_start: 0.8627 (t) cc_final: 0.8381 (t) REVERT: C 391 SER cc_start: 0.7905 (m) cc_final: 0.7547 (t) REVERT: D 391 SER cc_start: 0.7857 (m) cc_final: 0.7574 (t) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 1.2333 time to fit residues: 101.5122 Evaluate side-chains 69 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 135 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 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 = 0.3531 r_free = 0.3531 target = 0.093088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064207 restraints weight = 25914.773| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.45 r_work: 0.2838 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13008 Z= 0.175 Angle : 0.588 13.049 17692 Z= 0.280 Chirality : 0.041 0.145 1956 Planarity : 0.003 0.037 2272 Dihedral : 6.808 115.828 1762 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.60 % Allowed : 15.23 % Favored : 84.16 % 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: 1.23 (0.22), residues: 1592 helix: 1.70 (0.18), residues: 878 sheet: 0.03 (0.44), residues: 178 loop : -0.32 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 382 HIS 0.004 0.001 HIS D 234 PHE 0.013 0.001 PHE A 148 TYR 0.010 0.001 TYR B 98 ARG 0.007 0.000 ARG B 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.48 seconds wall clock time: 61 minutes 11.69 seconds (3671.69 seconds total)