Starting phenix.real_space_refine (version: dev) on Mon Feb 20 21:37:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/02_2023/7ebf_31053.pdb" } resolution = 2.63 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3263 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 396} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3263 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 396} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3263 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 396} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3263 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 396} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 7.48, per 1000 atoms: 0.57 Number of scatterers: 13052 At special positions: 0 Unit cell: (96.291, 147.317, 92.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2404 8.00 N 2276 7.00 C 8340 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 - 3.50 Amino acid : False - 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: 5.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 55.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.901A pdb=" N GLN A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 151 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.583A pdb=" N HIS A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 266' Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 292 through 307 removed outlier: 4.311A pdb=" N ALA A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.996A pdb=" N CYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 39 through 47 Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.901A pdb=" N GLN B 58 " --> pdb=" O HIS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 220 through 239 Processing helix chain 'B' and resid 261 through 266 removed outlier: 3.583A pdb=" N HIS B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 266 " --> pdb=" O HIS B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 266' Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 292 through 307 removed outlier: 4.310A pdb=" N ALA B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.995A pdb=" N CYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 445 through 457 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 54 through 74 removed outlier: 3.902A pdb=" N GLN C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 151 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 220 through 239 Processing helix chain 'C' and resid 261 through 266 removed outlier: 3.584A pdb=" N HIS C 265 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR C 266 " --> pdb=" O HIS C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 266' Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 292 through 307 removed outlier: 4.309A pdb=" N ALA C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.995A pdb=" N CYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 396 No H-bonds generated for 'chain 'C' and resid 394 through 396' Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 445 through 457 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 54 through 74 removed outlier: 3.902A pdb=" N GLN D 58 " --> pdb=" O HIS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 151 Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 220 through 239 Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.583A pdb=" N HIS D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR D 266 " --> pdb=" O HIS D 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 266' Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 292 through 307 removed outlier: 4.310A pdb=" N ALA D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 321 Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.995A pdb=" N CYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 396 No H-bonds generated for 'chain 'D' and resid 394 through 396' Processing helix chain 'D' and resid 407 through 422 Processing helix chain 'D' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 5.820A pdb=" N SER A 77 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 427 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN A 461 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR A 429 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 399 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASN A 430 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET A 401 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 244 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TRP A 400 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 246 " --> pdb=" O TRP A 400 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU A 402 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR A 248 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 198 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 247 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 200 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 removed outlier: 5.551A pdb=" N LYS A 216 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78 removed outlier: 5.819A pdb=" N SER B 77 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B 427 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN B 461 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B 429 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 399 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASN B 430 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET B 401 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA B 244 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP B 400 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA B 246 " --> pdb=" O TRP B 400 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU B 402 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR B 248 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 198 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 247 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 200 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 216 through 218 removed outlier: 5.551A pdb=" N LYS B 216 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 5.820A pdb=" N SER C 77 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 427 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN C 461 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR C 429 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 399 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASN C 430 " --> pdb=" O ILE C 399 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET C 401 " --> pdb=" O ASN C 430 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 244 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TRP C 400 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 246 " --> pdb=" O TRP C 400 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU C 402 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR C 248 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 198 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG C 247 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 200 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 216 through 218 removed outlier: 5.552A pdb=" N LYS C 216 " --> pdb=" O ALA C 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 78 removed outlier: 5.819A pdb=" N SER D 77 " --> pdb=" O GLN D 461 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU D 427 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN D 461 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR D 429 " --> pdb=" O GLN D 461 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 399 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN D 430 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET D 401 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA D 244 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP D 400 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA D 246 " --> pdb=" O TRP D 400 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLU D 402 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR D 248 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 198 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG D 247 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 200 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 216 through 218 removed outlier: 5.551A pdb=" N LYS D 216 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 270 through 271 665 hydrogen bonds defined for protein. 1935 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: 3.95 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4237 1.34 - 1.46: 3029 1.46 - 1.58: 5998 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 13320 Sorted by residual: bond pdb=" C GLU C 28 " pdb=" N PRO C 29 " ideal model delta sigma weight residual 1.336 1.347 -0.011 1.08e-02 8.57e+03 1.11e+00 bond pdb=" C GLU A 28 " pdb=" N PRO A 29 " ideal model delta sigma weight residual 1.336 1.347 -0.011 1.08e-02 8.57e+03 1.04e+00 bond pdb=" CA VAL A 127 " pdb=" CB VAL A 127 " ideal model delta sigma weight residual 1.534 1.541 -0.006 6.80e-03 2.16e+04 8.73e-01 bond pdb=" CA VAL D 127 " pdb=" CB VAL D 127 " ideal model delta sigma weight residual 1.534 1.540 -0.006 6.80e-03 2.16e+04 7.36e-01 bond pdb=" CA VAL C 127 " pdb=" CB VAL C 127 " ideal model delta sigma weight residual 1.534 1.540 -0.006 6.80e-03 2.16e+04 7.25e-01 ... (remaining 13315 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 421 107.41 - 114.07: 7612 114.07 - 120.72: 5521 120.72 - 127.38: 4222 127.38 - 134.03: 168 Bond angle restraints: 17944 Sorted by residual: angle pdb=" CA LEU B 331 " pdb=" CB LEU B 331 " pdb=" CG LEU B 331 " ideal model delta sigma weight residual 116.30 123.31 -7.01 3.50e+00 8.16e-02 4.01e+00 angle pdb=" CA LEU A 331 " pdb=" CB LEU A 331 " pdb=" CG LEU A 331 " ideal model delta sigma weight residual 116.30 123.30 -7.00 3.50e+00 8.16e-02 4.00e+00 angle pdb=" CA LEU C 331 " pdb=" CB LEU C 331 " pdb=" CG LEU C 331 " ideal model delta sigma weight residual 116.30 123.29 -6.99 3.50e+00 8.16e-02 3.99e+00 angle pdb=" CA LEU D 331 " pdb=" CB LEU D 331 " pdb=" CG LEU D 331 " ideal model delta sigma weight residual 116.30 123.24 -6.94 3.50e+00 8.16e-02 3.93e+00 angle pdb=" C ALA D 297 " pdb=" N ALA D 298 " pdb=" CA ALA D 298 " ideal model delta sigma weight residual 120.29 122.62 -2.33 1.42e+00 4.96e-01 2.69e+00 ... (remaining 17939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 7562 17.62 - 35.25: 338 35.25 - 52.87: 56 52.87 - 70.49: 16 70.49 - 88.11: 12 Dihedral angle restraints: 7984 sinusoidal: 3228 harmonic: 4756 Sorted by residual: dihedral pdb=" CA GLU D 285 " pdb=" CB GLU D 285 " pdb=" CG GLU D 285 " pdb=" CD GLU D 285 " ideal model delta sinusoidal sigma weight residual 180.00 122.42 57.58 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU A 285 " pdb=" CB GLU A 285 " pdb=" CG GLU A 285 " pdb=" CD GLU A 285 " ideal model delta sinusoidal sigma weight residual 180.00 122.44 57.56 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU C 285 " pdb=" CB GLU C 285 " pdb=" CG GLU C 285 " pdb=" CD GLU C 285 " ideal model delta sinusoidal sigma weight residual 180.00 122.45 57.55 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 7981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1126 0.025 - 0.050: 514 0.050 - 0.075: 181 0.075 - 0.101: 78 0.101 - 0.126: 49 Chirality restraints: 1948 Sorted by residual: chirality pdb=" CA VAL A 219 " pdb=" N VAL A 219 " pdb=" C VAL A 219 " pdb=" CB VAL A 219 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL D 219 " pdb=" N VAL D 219 " pdb=" C VAL D 219 " pdb=" CB VAL D 219 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE C 170 " pdb=" N ILE C 170 " pdb=" C ILE C 170 " pdb=" CB ILE C 170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 1945 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 28 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO B 29 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 28 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO C 29 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 28 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO D 29 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.016 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3639 2.82 - 3.34: 12524 3.34 - 3.86: 23176 3.86 - 4.38: 26458 4.38 - 4.90: 44140 Nonbonded interactions: 109937 Sorted by model distance: nonbonded pdb=" O ALA C 204 " pdb=" OG1 THR C 207 " model vdw 2.294 2.440 nonbonded pdb=" O ALA B 204 " pdb=" OG1 THR B 207 " model vdw 2.294 2.440 nonbonded pdb=" O ALA D 204 " pdb=" OG1 THR D 207 " model vdw 2.295 2.440 nonbonded pdb=" O ALA A 204 " pdb=" OG1 THR A 207 " model vdw 2.296 2.440 nonbonded pdb=" OE2 GLU A 201 " pdb=" NH2 ARG A 247 " model vdw 2.322 2.520 ... (remaining 109932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 8340 2.51 5 N 2276 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.620 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: 8.310 Check model and map are aligned: 0.190 Process input model: 35.180 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.002 0.035 13320 Z= 0.121 Angle : 0.417 7.013 17944 Z= 0.223 Chirality : 0.037 0.126 1948 Planarity : 0.003 0.029 2276 Dihedral : 11.012 88.114 4896 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1576 helix: 1.91 (0.18), residues: 840 sheet: 1.53 (0.39), residues: 164 loop : -0.30 (0.24), residues: 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.538 Fit side-chains outliers start: 28 outliers final: 4 residues processed: 252 average time/residue: 1.6111 time to fit residues: 434.6069 Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2466 time to fit residues: 3.6272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 461 GLN B 461 GLN C 461 GLN D 461 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13320 Z= 0.173 Angle : 0.467 7.407 17944 Z= 0.244 Chirality : 0.039 0.146 1948 Planarity : 0.003 0.032 2276 Dihedral : 3.620 14.343 1748 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 4.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1576 helix: 1.70 (0.18), residues: 864 sheet: 1.50 (0.37), residues: 160 loop : -0.62 (0.23), residues: 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 143 time to evaluate : 1.634 Fit side-chains outliers start: 57 outliers final: 17 residues processed: 171 average time/residue: 1.3224 time to fit residues: 246.3103 Evaluate side-chains 151 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.6853 time to fit residues: 15.4889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13320 Z= 0.180 Angle : 0.467 7.152 17944 Z= 0.245 Chirality : 0.039 0.147 1948 Planarity : 0.003 0.035 2276 Dihedral : 3.751 14.529 1748 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1576 helix: 1.60 (0.18), residues: 860 sheet: 1.61 (0.37), residues: 152 loop : -0.49 (0.24), residues: 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 144 time to evaluate : 1.457 Fit side-chains outliers start: 51 outliers final: 15 residues processed: 171 average time/residue: 1.2282 time to fit residues: 229.8909 Evaluate side-chains 136 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.5898 time to fit residues: 6.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN B 410 GLN C 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 13320 Z= 0.138 Angle : 0.435 6.898 17944 Z= 0.229 Chirality : 0.039 0.139 1948 Planarity : 0.003 0.035 2276 Dihedral : 3.614 13.648 1748 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1576 helix: 1.62 (0.18), residues: 872 sheet: 1.68 (0.38), residues: 152 loop : -0.39 (0.24), residues: 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 137 time to evaluate : 1.499 Fit side-chains outliers start: 61 outliers final: 21 residues processed: 178 average time/residue: 1.2574 time to fit residues: 244.9915 Evaluate side-chains 157 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.4229 time to fit residues: 5.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN C 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13320 Z= 0.247 Angle : 0.530 7.445 17944 Z= 0.278 Chirality : 0.041 0.148 1948 Planarity : 0.004 0.035 2276 Dihedral : 4.088 16.123 1748 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1576 helix: 1.29 (0.18), residues: 868 sheet: 1.38 (0.39), residues: 156 loop : -0.49 (0.25), residues: 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 1.428 Fit side-chains outliers start: 55 outliers final: 27 residues processed: 171 average time/residue: 1.3377 time to fit residues: 248.9898 Evaluate side-chains 150 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.5477 time to fit residues: 6.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 158 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 410 GLN C 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13320 Z= 0.164 Angle : 0.466 7.044 17944 Z= 0.245 Chirality : 0.040 0.137 1948 Planarity : 0.003 0.035 2276 Dihedral : 3.839 14.684 1748 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1576 helix: 1.40 (0.18), residues: 872 sheet: 1.63 (0.40), residues: 152 loop : -0.46 (0.24), residues: 552 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.581 Fit side-chains outliers start: 47 outliers final: 26 residues processed: 158 average time/residue: 1.1294 time to fit residues: 197.1415 Evaluate side-chains 145 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.4363 time to fit residues: 5.8552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN B 410 GLN C 133 HIS D 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13320 Z= 0.128 Angle : 0.428 6.865 17944 Z= 0.225 Chirality : 0.039 0.134 1948 Planarity : 0.003 0.035 2276 Dihedral : 3.616 13.237 1748 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1576 helix: 1.54 (0.18), residues: 872 sheet: 1.71 (0.40), residues: 152 loop : -0.41 (0.24), residues: 552 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.644 Fit side-chains outliers start: 43 outliers final: 25 residues processed: 156 average time/residue: 1.1421 time to fit residues: 196.8444 Evaluate side-chains 148 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 0.2134 time to fit residues: 4.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.0060 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN C 133 HIS D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 13320 Z= 0.144 Angle : 0.439 6.916 17944 Z= 0.231 Chirality : 0.039 0.137 1948 Planarity : 0.003 0.036 2276 Dihedral : 3.645 13.432 1748 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1576 helix: 1.52 (0.18), residues: 872 sheet: 1.75 (0.41), residues: 152 loop : -0.40 (0.24), residues: 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 124 time to evaluate : 1.673 Fit side-chains outliers start: 45 outliers final: 28 residues processed: 154 average time/residue: 1.1682 time to fit residues: 199.3751 Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 9 average time/residue: 0.5537 time to fit residues: 8.0638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN C 133 HIS D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13320 Z= 0.164 Angle : 0.459 7.074 17944 Z= 0.241 Chirality : 0.040 0.138 1948 Planarity : 0.003 0.037 2276 Dihedral : 3.730 13.833 1748 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1576 helix: 1.49 (0.18), residues: 872 sheet: 1.71 (0.41), residues: 152 loop : -0.39 (0.24), residues: 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.541 Fit side-chains outliers start: 39 outliers final: 26 residues processed: 143 average time/residue: 1.0526 time to fit residues: 167.6546 Evaluate side-chains 142 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.6704 time to fit residues: 7.5838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN B 410 GLN C 133 HIS D 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13320 Z= 0.250 Angle : 0.529 7.476 17944 Z= 0.279 Chirality : 0.042 0.143 1948 Planarity : 0.004 0.036 2276 Dihedral : 4.140 15.902 1748 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1576 helix: 1.36 (0.18), residues: 860 sheet: 1.03 (0.40), residues: 164 loop : -0.46 (0.24), residues: 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.543 Fit side-chains outliers start: 31 outliers final: 23 residues processed: 136 average time/residue: 1.1054 time to fit residues: 166.6493 Evaluate side-chains 132 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.8583 time to fit residues: 5.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.0670 chunk 130 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 410 GLN B 410 GLN C 133 HIS C 410 GLN D 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145944 restraints weight = 15672.944| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.75 r_work: 0.3623 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 13320 Z= 0.187 Angle : 0.485 7.234 17944 Z= 0.256 Chirality : 0.040 0.138 1948 Planarity : 0.003 0.037 2276 Dihedral : 3.966 14.979 1748 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1576 helix: 1.44 (0.18), residues: 860 sheet: 1.08 (0.41), residues: 164 loop : -0.43 (0.24), residues: 552 =============================================================================== Job complete usr+sys time: 4510.35 seconds wall clock time: 81 minutes 4.34 seconds (4864.34 seconds total)