Starting phenix.real_space_refine on Fri Mar 15 23:24:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/03_2024/7ebf_31053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/03_2024/7ebf_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_31053/03_2024/7ebf_31053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/03_2024/7ebf_31053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/03_2024/7ebf_31053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ebf_31053/03_2024/7ebf_31053.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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-5265/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: 7.02, per 1000 atoms: 0.54 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: 5.29 Conformation dependent library (CDL) restraints added in 2.1 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: 1.25 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: 3.87 Time building geometry restraints manager: 5.74 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 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: 2.700 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: 7.840 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 36.630 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 % Allowed : 4.52 % Favored : 93.37 % 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: 1.61 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 31 HIS 0.003 0.001 HIS D 199 PHE 0.007 0.001 PHE B 462 TYR 0.005 0.001 TYR C 378 ARG 0.002 0.000 ARG A 193 *********************** 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 : 1.504 Fit side-chains REVERT: A 129 ASN cc_start: 0.7386 (m-40) cc_final: 0.7186 (m-40) REVERT: A 213 MET cc_start: 0.2623 (ttt) cc_final: 0.2310 (ptp) REVERT: A 285 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5444 (mp0) REVERT: A 336 THR cc_start: 0.7130 (m) cc_final: 0.6926 (t) REVERT: A 358 THR cc_start: 0.7519 (m) cc_final: 0.7293 (t) REVERT: B 285 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5494 (mp0) REVERT: B 358 THR cc_start: 0.7642 (m) cc_final: 0.7398 (t) REVERT: C 213 MET cc_start: 0.2610 (ttt) cc_final: 0.2316 (ptp) REVERT: C 285 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: C 336 THR cc_start: 0.7055 (m) cc_final: 0.6828 (t) REVERT: C 358 THR cc_start: 0.7635 (m) cc_final: 0.7431 (t) REVERT: D 129 ASN cc_start: 0.7392 (m-40) cc_final: 0.7178 (m-40) REVERT: D 213 MET cc_start: 0.3053 (ttt) cc_final: 0.2407 (ptt) REVERT: D 285 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5229 (mp0) REVERT: D 336 THR cc_start: 0.7049 (m) cc_final: 0.6814 (t) REVERT: D 358 THR cc_start: 0.7622 (m) cc_final: 0.7418 (t) outliers start: 28 outliers final: 4 residues processed: 252 average time/residue: 1.5214 time to fit residues: 410.4425 Evaluate side-chains 149 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 430 ASN 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: 0.7596 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13320 Z= 0.170 Angle : 0.464 7.306 17944 Z= 0.242 Chirality : 0.039 0.147 1948 Planarity : 0.004 0.031 2276 Dihedral : 5.095 59.854 1768 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.22 % Allowed : 11.75 % Favored : 84.04 % 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: 1.37 (0.20), residues: 1576 helix: 1.76 (0.18), residues: 864 sheet: 1.51 (0.37), residues: 160 loop : -0.64 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 31 HIS 0.004 0.001 HIS A 347 PHE 0.009 0.001 PHE D 80 TYR 0.011 0.001 TYR A 162 ARG 0.003 0.000 ARG B 372 *********************** 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 203 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 1.499 Fit side-chains REVERT: A 21 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6042 (pp20) REVERT: A 132 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 285 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5593 (mp0) REVERT: A 358 THR cc_start: 0.7854 (m) cc_final: 0.7459 (t) REVERT: B 21 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.6030 (pp20) REVERT: B 285 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: B 358 THR cc_start: 0.7831 (m) cc_final: 0.7530 (t) REVERT: B 372 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7223 (ttm-80) REVERT: C 132 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: C 285 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5547 (mp0) REVERT: C 336 THR cc_start: 0.7236 (m) cc_final: 0.7021 (t) REVERT: C 358 THR cc_start: 0.7851 (m) cc_final: 0.7485 (t) REVERT: C 372 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7237 (ttm-80) REVERT: D 129 ASN cc_start: 0.7429 (m-40) cc_final: 0.7224 (m-40) REVERT: D 132 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: D 213 MET cc_start: 0.2845 (ttt) cc_final: 0.2320 (ptt) REVERT: D 285 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5393 (mp0) REVERT: D 358 THR cc_start: 0.7857 (m) cc_final: 0.7490 (t) outliers start: 56 outliers final: 14 residues processed: 176 average time/residue: 1.3545 time to fit residues: 258.2091 Evaluate side-chains 152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 430 ASN 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: 0.6980 chunk 123 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1956 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= 0.164 Angle : 0.449 7.098 17944 Z= 0.234 Chirality : 0.039 0.145 1948 Planarity : 0.003 0.035 2276 Dihedral : 5.100 59.975 1768 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.14 % Allowed : 12.35 % Favored : 83.51 % 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 (0.20), residues: 1576 helix: 1.69 (0.18), residues: 864 sheet: 1.68 (0.37), residues: 152 loop : -0.48 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 135 HIS 0.004 0.001 HIS A 347 PHE 0.012 0.001 PHE B 238 TYR 0.011 0.001 TYR B 162 ARG 0.004 0.000 ARG A 390 *********************** 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 201 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 1.582 Fit side-chains REVERT: A 21 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6039 (pp20) REVERT: A 285 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5594 (mp0) REVERT: A 358 THR cc_start: 0.7864 (m) cc_final: 0.7417 (t) REVERT: A 410 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: B 21 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.6042 (pp20) REVERT: B 285 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: B 358 THR cc_start: 0.7780 (m) cc_final: 0.7426 (t) REVERT: B 372 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7235 (ttm-80) REVERT: C 21 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: C 285 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: C 358 THR cc_start: 0.7885 (m) cc_final: 0.7459 (t) REVERT: C 372 ARG cc_start: 0.7484 (tpp80) cc_final: 0.7252 (ttm-80) REVERT: D 129 ASN cc_start: 0.7446 (m-40) cc_final: 0.7234 (m-40) REVERT: D 213 MET cc_start: 0.2919 (ttt) cc_final: 0.2476 (ptt) REVERT: D 285 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: D 358 THR cc_start: 0.7849 (m) cc_final: 0.7457 (t) outliers start: 55 outliers final: 17 residues processed: 173 average time/residue: 1.1952 time to fit residues: 226.1820 Evaluate side-chains 154 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13320 Z= 0.151 Angle : 0.441 6.843 17944 Z= 0.231 Chirality : 0.039 0.139 1948 Planarity : 0.003 0.035 2276 Dihedral : 5.005 59.429 1768 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.52 % Allowed : 12.20 % Favored : 83.28 % 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: 1.68 (0.18), residues: 868 sheet: 1.68 (0.38), residues: 152 loop : -0.46 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.003 0.001 HIS D 224 PHE 0.014 0.001 PHE B 238 TYR 0.009 0.001 TYR B 162 ARG 0.005 0.000 ARG B 390 *********************** 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 201 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 141 time to evaluate : 1.490 Fit side-chains REVERT: A 21 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5966 (pp20) REVERT: A 167 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7266 (mmp80) REVERT: A 285 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: A 358 THR cc_start: 0.7892 (m) cc_final: 0.7417 (t) REVERT: A 410 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6266 (tt0) REVERT: B 21 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5981 (pp20) REVERT: B 132 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: B 167 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7253 (mmp80) REVERT: B 285 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5730 (mp0) REVERT: B 358 THR cc_start: 0.7810 (m) cc_final: 0.7443 (t) REVERT: B 372 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7249 (ttm-80) REVERT: C 21 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.6053 (pp20) REVERT: C 132 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: C 285 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5757 (mp0) REVERT: C 358 THR cc_start: 0.7894 (m) cc_final: 0.7469 (t) REVERT: C 372 ARG cc_start: 0.7469 (tpp80) cc_final: 0.7237 (ttm-80) REVERT: D 167 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7220 (mmp80) REVERT: D 213 MET cc_start: 0.2766 (ttt) cc_final: 0.2392 (ptt) REVERT: D 285 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: D 302 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.3995 (tt0) REVERT: D 358 THR cc_start: 0.7870 (m) cc_final: 0.7457 (t) outliers start: 60 outliers final: 21 residues processed: 174 average time/residue: 1.2212 time to fit residues: 232.7999 Evaluate side-chains 165 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN 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: 3.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13320 Z= 0.362 Angle : 0.603 7.804 17944 Z= 0.318 Chirality : 0.044 0.148 1948 Planarity : 0.004 0.036 2276 Dihedral : 5.592 54.919 1768 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.20 % Allowed : 11.75 % Favored : 83.06 % 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: 0.63 (0.20), residues: 1576 helix: 1.09 (0.17), residues: 864 sheet: 0.93 (0.38), residues: 164 loop : -0.74 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 400 HIS 0.005 0.001 HIS A 347 PHE 0.016 0.003 PHE D 80 TYR 0.015 0.002 TYR B 408 ARG 0.005 0.001 ARG C 390 *********************** 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 203 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 134 time to evaluate : 1.500 Fit side-chains REVERT: A 21 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5990 (pp20) REVERT: A 132 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: A 167 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6692 (mmp80) REVERT: A 285 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: A 358 THR cc_start: 0.7961 (m) cc_final: 0.7754 (m) REVERT: A 410 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: B 21 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: B 132 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: B 167 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6697 (mmp80) REVERT: B 285 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: B 358 THR cc_start: 0.7980 (m) cc_final: 0.7596 (t) REVERT: C 21 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: C 132 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: C 167 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6836 (mmp80) REVERT: C 285 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: C 358 THR cc_start: 0.8003 (m) cc_final: 0.7582 (t) REVERT: D 21 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5963 (pp20) REVERT: D 129 ASN cc_start: 0.7496 (m-40) cc_final: 0.7191 (m-40) REVERT: D 132 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: D 167 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6807 (mmp80) REVERT: D 285 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5887 (mp0) REVERT: D 302 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4102 (tt0) REVERT: D 358 THR cc_start: 0.8009 (m) cc_final: 0.7594 (t) REVERT: D 372 ARG cc_start: 0.7527 (tpp80) cc_final: 0.7063 (mtm-85) REVERT: D 410 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6566 (tt0) outliers start: 69 outliers final: 32 residues processed: 179 average time/residue: 1.3099 time to fit residues: 254.5742 Evaluate side-chains 174 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13320 Z= 0.165 Angle : 0.474 7.125 17944 Z= 0.249 Chirality : 0.040 0.137 1948 Planarity : 0.003 0.035 2276 Dihedral : 5.186 54.963 1768 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.59 % Allowed : 13.70 % Favored : 81.70 % 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: 1.08 (0.21), residues: 1576 helix: 1.43 (0.18), residues: 864 sheet: 1.57 (0.40), residues: 152 loop : -0.60 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 400 HIS 0.004 0.001 HIS D 224 PHE 0.017 0.002 PHE C 238 TYR 0.008 0.001 TYR B 162 ARG 0.002 0.000 ARG D 390 *********************** 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 192 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 131 time to evaluate : 1.449 Fit side-chains REVERT: A 132 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 167 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7272 (mmp80) REVERT: A 285 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: A 358 THR cc_start: 0.7960 (m) cc_final: 0.7518 (t) REVERT: A 410 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: B 132 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 167 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7276 (mmp80) REVERT: B 285 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5972 (mp0) REVERT: B 358 THR cc_start: 0.7933 (m) cc_final: 0.7527 (t) REVERT: C 21 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5940 (pp20) REVERT: C 167 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7109 (mmp80) REVERT: C 285 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: C 358 THR cc_start: 0.7938 (m) cc_final: 0.7536 (t) REVERT: C 410 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: D 21 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5935 (pp20) REVERT: D 167 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7195 (mmp80) REVERT: D 213 MET cc_start: 0.2811 (ttt) cc_final: 0.2444 (ptt) REVERT: D 285 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5797 (mp0) REVERT: D 302 GLU cc_start: 0.5140 (OUTLIER) cc_final: 0.4053 (tt0) REVERT: D 358 THR cc_start: 0.7949 (m) cc_final: 0.7561 (t) REVERT: D 372 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7047 (mtm-85) REVERT: D 410 GLN cc_start: 0.6864 (pt0) cc_final: 0.6357 (tt0) outliers start: 61 outliers final: 26 residues processed: 169 average time/residue: 1.2542 time to fit residues: 230.9008 Evaluate side-chains 168 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.2405 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= 0.145 Angle : 0.446 7.020 17944 Z= 0.235 Chirality : 0.039 0.137 1948 Planarity : 0.003 0.034 2276 Dihedral : 4.988 54.702 1768 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.07 % Allowed : 14.46 % Favored : 81.48 % 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: 1.25 (0.21), residues: 1576 helix: 1.55 (0.18), residues: 868 sheet: 1.66 (0.40), residues: 152 loop : -0.52 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 400 HIS 0.004 0.001 HIS C 199 PHE 0.020 0.001 PHE A 238 TYR 0.004 0.001 TYR B 408 ARG 0.002 0.000 ARG B 47 *********************** 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 189 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.549 Fit side-chains REVERT: A 167 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7298 (mmp80) REVERT: A 285 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: A 358 THR cc_start: 0.7934 (m) cc_final: 0.7488 (t) REVERT: A 410 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6234 (tt0) REVERT: B 21 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5945 (pp20) REVERT: B 167 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7296 (mmp80) REVERT: B 285 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: B 358 THR cc_start: 0.7895 (m) cc_final: 0.7492 (t) REVERT: C 21 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5939 (pp20) REVERT: C 167 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7198 (mmp80) REVERT: C 285 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: C 358 THR cc_start: 0.7908 (m) cc_final: 0.7493 (t) REVERT: D 21 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5938 (pp20) REVERT: D 132 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: D 167 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7241 (mmp80) REVERT: D 213 MET cc_start: 0.2676 (ttt) cc_final: 0.2356 (ptt) REVERT: D 285 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5634 (mp0) REVERT: D 302 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4035 (tt0) REVERT: D 358 THR cc_start: 0.7934 (m) cc_final: 0.7526 (t) REVERT: D 372 ARG cc_start: 0.7382 (tpp80) cc_final: 0.6977 (mtm-85) REVERT: D 410 GLN cc_start: 0.6843 (pt0) cc_final: 0.6286 (tt0) outliers start: 54 outliers final: 29 residues processed: 169 average time/residue: 1.2866 time to fit residues: 237.0465 Evaluate side-chains 172 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.2449 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= 0.157 Angle : 0.448 6.952 17944 Z= 0.236 Chirality : 0.039 0.137 1948 Planarity : 0.003 0.034 2276 Dihedral : 4.927 54.473 1768 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.22 % Allowed : 14.53 % Favored : 81.25 % 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: 1.26 (0.21), residues: 1576 helix: 1.55 (0.18), residues: 868 sheet: 1.70 (0.41), residues: 152 loop : -0.52 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 400 HIS 0.003 0.001 HIS A 224 PHE 0.023 0.002 PHE D 238 TYR 0.005 0.001 TYR A 408 ARG 0.001 0.000 ARG B 372 *********************** 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 185 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 1.525 Fit side-chains REVERT: A 132 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 167 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7320 (mmp80) REVERT: A 285 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: A 358 THR cc_start: 0.7938 (m) cc_final: 0.7478 (t) REVERT: A 410 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6225 (tt0) REVERT: B 21 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5941 (pp20) REVERT: B 167 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7252 (mmp80) REVERT: B 285 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: B 358 THR cc_start: 0.7875 (m) cc_final: 0.7448 (t) REVERT: C 21 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5969 (pp20) REVERT: C 167 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7224 (mmp80) REVERT: C 285 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5911 (mp0) REVERT: C 358 THR cc_start: 0.7913 (m) cc_final: 0.7480 (t) REVERT: D 21 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5980 (pp20) REVERT: D 132 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: D 167 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7245 (mmp80) REVERT: D 213 MET cc_start: 0.2672 (ttt) cc_final: 0.2372 (ptt) REVERT: D 285 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: D 302 GLU cc_start: 0.5161 (OUTLIER) cc_final: 0.4010 (tt0) REVERT: D 358 THR cc_start: 0.7942 (m) cc_final: 0.7519 (t) REVERT: D 372 ARG cc_start: 0.7374 (tpp80) cc_final: 0.6965 (mtm-85) REVERT: D 410 GLN cc_start: 0.6825 (pt0) cc_final: 0.6301 (tt0) outliers start: 56 outliers final: 30 residues processed: 164 average time/residue: 1.1991 time to fit residues: 215.6996 Evaluate side-chains 170 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN 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: 3.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13320 Z= 0.178 Angle : 0.466 7.049 17944 Z= 0.244 Chirality : 0.040 0.138 1948 Planarity : 0.003 0.034 2276 Dihedral : 4.937 53.775 1768 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.99 % Allowed : 14.68 % Favored : 81.33 % 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: 1.21 (0.21), residues: 1576 helix: 1.50 (0.18), residues: 868 sheet: 1.67 (0.41), residues: 152 loop : -0.52 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 400 HIS 0.003 0.001 HIS C 224 PHE 0.031 0.002 PHE D 238 TYR 0.006 0.001 TYR A 408 ARG 0.002 0.000 ARG B 157 *********************** 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 172 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 119 time to evaluate : 1.509 Fit side-chains REVERT: A 132 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: A 167 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7247 (mmp80) REVERT: A 285 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: A 358 THR cc_start: 0.7938 (m) cc_final: 0.7475 (t) REVERT: A 410 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: B 21 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5949 (pp20) REVERT: B 167 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7251 (mmp80) REVERT: B 285 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: B 358 THR cc_start: 0.7916 (m) cc_final: 0.7495 (t) REVERT: C 21 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5960 (pp20) REVERT: C 167 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7119 (mmp80) REVERT: C 285 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5853 (mp0) REVERT: C 358 THR cc_start: 0.7918 (m) cc_final: 0.7484 (t) REVERT: D 21 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: D 132 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: D 167 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7172 (mmp80) REVERT: D 213 MET cc_start: 0.2715 (ttt) cc_final: 0.2338 (ptt) REVERT: D 285 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: D 302 GLU cc_start: 0.5067 (OUTLIER) cc_final: 0.3965 (tt0) REVERT: D 358 THR cc_start: 0.7954 (m) cc_final: 0.7513 (t) REVERT: D 372 ARG cc_start: 0.7373 (tpp80) cc_final: 0.6965 (mtm-85) outliers start: 53 outliers final: 35 residues processed: 150 average time/residue: 1.2505 time to fit residues: 205.2292 Evaluate side-chains 169 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13320 Z= 0.188 Angle : 0.474 7.125 17944 Z= 0.248 Chirality : 0.040 0.138 1948 Planarity : 0.003 0.034 2276 Dihedral : 4.936 52.302 1768 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.07 % Allowed : 14.76 % Favored : 81.17 % 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: 1.18 (0.21), residues: 1576 helix: 1.50 (0.18), residues: 864 sheet: 1.63 (0.41), residues: 152 loop : -0.56 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 400 HIS 0.003 0.001 HIS C 224 PHE 0.028 0.002 PHE A 238 TYR 0.007 0.001 TYR A 408 ARG 0.002 0.000 ARG B 157 ********************** 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 174 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 120 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: A 167 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7225 (mmp80) REVERT: A 285 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5788 (mp0) REVERT: A 358 THR cc_start: 0.7964 (m) cc_final: 0.7508 (t) REVERT: A 410 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: B 21 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5960 (pp20) REVERT: B 167 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7221 (mmp80) REVERT: B 285 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: B 358 THR cc_start: 0.7925 (m) cc_final: 0.7486 (t) REVERT: C 21 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5976 (pp20) REVERT: C 132 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: C 167 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7144 (mmp80) REVERT: C 285 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: C 358 THR cc_start: 0.7915 (m) cc_final: 0.7474 (t) REVERT: D 21 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5998 (pp20) REVERT: D 132 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: D 167 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7135 (mmp80) REVERT: D 213 MET cc_start: 0.2797 (ttt) cc_final: 0.2316 (ptt) REVERT: D 285 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: D 358 THR cc_start: 0.7950 (m) cc_final: 0.7500 (t) REVERT: D 372 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6924 (mtm-85) outliers start: 54 outliers final: 36 residues processed: 155 average time/residue: 1.2505 time to fit residues: 212.0982 Evaluate side-chains 167 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 116 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.178269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143261 restraints weight = 15610.874| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.78 r_work: 0.3588 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13320 Z= 0.313 Angle : 0.570 7.846 17944 Z= 0.300 Chirality : 0.043 0.143 1948 Planarity : 0.004 0.035 2276 Dihedral : 5.307 48.755 1768 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.22 % Allowed : 14.98 % Favored : 80.80 % 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: 0.77 (0.20), residues: 1576 helix: 1.17 (0.17), residues: 864 sheet: 1.01 (0.40), residues: 164 loop : -0.63 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.004 0.001 HIS B 313 PHE 0.028 0.003 PHE A 238 TYR 0.013 0.002 TYR A 408 ARG 0.003 0.001 ARG B 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.84 seconds wall clock time: 84 minutes 18.61 seconds (5058.61 seconds total)