Starting phenix.real_space_refine (version: dev) on Fri May 13 15:16:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/05_2022/7ebf_31053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/05_2022/7ebf_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_31053/05_2022/7ebf_31053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/05_2022/7ebf_31053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/05_2022/7ebf_31053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/05_2022/7ebf_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 7.14, per 1000 atoms: 0.55 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: 5.67 Conformation dependent library (CDL) restraints added in 2.0 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: 0.84 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: 3.98 Time building geometry restraints manager: 6.08 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: 1.200 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: 8.190 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.100 Process input model: 37.390 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- 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 : 5.92 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 : 1.481 Fit side-chains outliers start: 28 outliers final: 4 residues processed: 252 average time/residue: 1.4676 time to fit residues: 397.4463 Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2438 time to fit residues: 3.5326 ------------------------------------------------------------------------------- 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 : 8.45 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 : 1.551 Fit side-chains outliers start: 57 outliers final: 17 residues processed: 171 average time/residue: 1.2651 time to fit residues: 236.3949 Evaluate side-chains 151 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.6791 time to fit residues: 15.4573 ------------------------------------------------------------------------------- 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: 7.9990 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: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13320 Z= 0.197 Angle : 0.483 7.361 17944 Z= 0.252 Chirality : 0.040 0.148 1948 Planarity : 0.004 0.034 2276 Dihedral : 3.831 15.004 1748 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.69 % 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: 1.23 (0.20), residues: 1576 helix: 1.55 (0.18), residues: 860 sheet: 1.58 (0.37), residues: 152 loop : -0.50 (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 188 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.723 Fit side-chains outliers start: 49 outliers final: 16 residues processed: 163 average time/residue: 1.2071 time to fit residues: 216.2202 Evaluate side-chains 133 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.6058 time to fit residues: 7.1031 ------------------------------------------------------------------------------- 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: 0.5980 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.0670 chunk 42 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN C 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2133 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= 0.121 Angle : 0.419 6.829 17944 Z= 0.220 Chirality : 0.038 0.137 1948 Planarity : 0.003 0.036 2276 Dihedral : 3.521 13.201 1748 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1576 helix: 1.66 (0.18), residues: 868 sheet: 1.70 (0.38), residues: 152 loop : -0.40 (0.24), residues: 556 *********************** 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 203 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 145 time to evaluate : 1.678 Fit side-chains outliers start: 58 outliers final: 19 residues processed: 181 average time/residue: 1.0778 time to fit residues: 215.7805 Evaluate side-chains 155 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 8 average time/residue: 0.2206 time to fit residues: 4.5772 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 13320 Z= 0.140 Angle : 0.435 6.883 17944 Z= 0.228 Chirality : 0.039 0.138 1948 Planarity : 0.003 0.037 2276 Dihedral : 3.542 13.018 1748 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.77 % 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: 1.40 (0.21), residues: 1576 helix: 1.61 (0.18), residues: 872 sheet: 1.74 (0.39), residues: 152 loop : -0.35 (0.24), 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 190 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.680 Fit side-chains outliers start: 50 outliers final: 26 residues processed: 166 average time/residue: 1.1340 time to fit residues: 208.0472 Evaluate side-chains 155 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 10 average time/residue: 0.5413 time to fit residues: 8.6385 ------------------------------------------------------------------------------- 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: 0.9980 chunk 142 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13320 Z= 0.182 Angle : 0.466 7.118 17944 Z= 0.244 Chirality : 0.040 0.141 1948 Planarity : 0.003 0.036 2276 Dihedral : 3.747 14.213 1748 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 1.28 (0.21), residues: 1576 helix: 1.51 (0.18), residues: 868 sheet: 1.72 (0.39), residues: 152 loop : -0.42 (0.24), residues: 556 *********************** 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 179 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 1.561 Fit side-chains outliers start: 55 outliers final: 26 residues processed: 161 average time/residue: 1.0671 time to fit residues: 190.4122 Evaluate side-chains 154 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.4641 time to fit residues: 7.2675 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 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 410 GLN B 410 GLN C 133 HIS D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13320 Z= 0.128 Angle : 0.426 6.868 17944 Z= 0.225 Chirality : 0.039 0.135 1948 Planarity : 0.003 0.037 2276 Dihedral : 3.572 12.860 1748 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 3.01 % 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: 1.38 (0.21), residues: 1576 helix: 1.56 (0.18), residues: 872 sheet: 1.82 (0.40), residues: 152 loop : -0.35 (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 180 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.617 Fit side-chains outliers start: 40 outliers final: 25 residues processed: 162 average time/residue: 1.0234 time to fit residues: 184.5326 Evaluate side-chains 148 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.2129 time to fit residues: 4.2709 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 13320 Z= 0.141 Angle : 0.430 6.920 17944 Z= 0.227 Chirality : 0.039 0.137 1948 Planarity : 0.003 0.037 2276 Dihedral : 3.588 13.031 1748 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 3.31 % 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: 1.41 (0.21), residues: 1576 helix: 1.60 (0.18), residues: 872 sheet: 1.83 (0.40), residues: 152 loop : -0.35 (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 173 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 1.539 Fit side-chains outliers start: 44 outliers final: 26 residues processed: 157 average time/residue: 0.9842 time to fit residues: 172.7187 Evaluate side-chains 152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.4401 time to fit residues: 6.0226 ------------------------------------------------------------------------------- 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: 8.9990 chunk 151 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 13320 Z= 0.317 Angle : 0.572 7.849 17944 Z= 0.302 Chirality : 0.044 0.145 1948 Planarity : 0.004 0.036 2276 Dihedral : 4.322 16.671 1748 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 0.83 (0.20), residues: 1576 helix: 1.12 (0.17), residues: 868 sheet: 1.33 (0.40), residues: 156 loop : -0.51 (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: 43 poor density : 114 time to evaluate : 1.612 Fit side-chains outliers start: 43 outliers final: 26 residues processed: 142 average time/residue: 1.0728 time to fit residues: 169.6616 Evaluate side-chains 134 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.4372 time to fit residues: 6.4230 ------------------------------------------------------------------------------- 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: 4.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 13320 Z= 0.282 Angle : 0.545 7.652 17944 Z= 0.288 Chirality : 0.043 0.142 1948 Planarity : 0.004 0.037 2276 Dihedral : 4.333 16.490 1748 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.96 % 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: 0.87 (0.21), residues: 1576 helix: 1.15 (0.17), residues: 860 sheet: 1.26 (0.41), residues: 156 loop : -0.43 (0.25), residues: 560 ********************** 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 140 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.687 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 135 average time/residue: 1.1773 time to fit residues: 176.0695 Evaluate side-chains 124 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 1.1641 time to fit residues: 7.3276 ------------------------------------------------------------------------------- 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: 9.9990 chunk 119 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.0010 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.179130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144366 restraints weight = 15622.471| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.77 r_work: 0.3705 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.3665 rms_B_bonded: 1.89 restraints_weight: 0.1250 r_work: 0.3638 rms_B_bonded: 2.24 restraints_weight: 0.0625 r_work: 0.3602 rms_B_bonded: 2.79 restraints_weight: 0.0312 r_work: 0.3553 rms_B_bonded: 3.64 restraints_weight: 0.0156 r_work: 0.3483 rms_B_bonded: 4.98 restraints_weight: 0.0078 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13320 Z= 0.242 Angle : 0.527 7.586 17944 Z= 0.279 Chirality : 0.042 0.140 1948 Planarity : 0.004 0.036 2276 Dihedral : 4.255 16.706 1748 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.88 % 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: 0.84 (0.21), residues: 1576 helix: 1.15 (0.17), residues: 868 sheet: 1.28 (0.41), residues: 156 loop : -0.53 (0.25), residues: 552 =============================================================================== Job complete usr+sys time: 3927.90 seconds wall clock time: 71 minutes 12.98 seconds (4272.98 seconds total)