Starting phenix.real_space_refine on Wed Mar 4 10:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_31053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_31053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_31053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_31053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ebf_31053/03_2026/7ebf_31053.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13052 Number of models: 1 Model: "" Number of chains: 1 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, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 2.08, per 1000 atoms: 0.16 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 579.4 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 55.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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: 2.26 Time building geometry restraints manager: 1.27 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: 0.00 - 1.40: 17708 1.40 - 2.81: 197 2.81 - 4.21: 27 4.21 - 5.61: 8 5.61 - 7.01: 4 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 3.040 nonbonded pdb=" O ALA B 204 " pdb=" OG1 THR B 207 " model vdw 2.294 3.040 nonbonded pdb=" O ALA D 204 " pdb=" OG1 THR D 207 " model vdw 2.295 3.040 nonbonded pdb=" O ALA A 204 " pdb=" OG1 THR A 207 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU A 201 " pdb=" NH2 ARG A 247 " model vdw 2.322 3.120 ... (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 Time spend for trying shortcut: 0.03 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- 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= 0.092 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 193 TYR 0.005 0.001 TYR C 378 PHE 0.007 0.001 PHE B 462 TRP 0.006 0.001 TRP A 31 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00187 (13320) covalent geometry : angle 0.41660 (17944) hydrogen bonds : bond 0.14215 ( 665) hydrogen bonds : angle 4.39589 ( 1935) *********************** 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 to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.490 Fit side-chains REVERT: A 213 MET cc_start: 0.2623 (ttt) cc_final: 0.2309 (ptp) REVERT: A 285 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5443 (mp0) REVERT: A 336 THR cc_start: 0.7130 (m) cc_final: 0.6927 (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: 0.5495 (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: 0.5552 (mp0) REVERT: C 336 THR cc_start: 0.7055 (m) cc_final: 0.6829 (t) REVERT: C 358 THR cc_start: 0.7635 (m) cc_final: 0.7432 (t) REVERT: D 129 ASN cc_start: 0.7392 (m-40) cc_final: 0.7179 (m-40) REVERT: D 213 MET cc_start: 0.3053 (ttt) cc_final: 0.2406 (ptt) REVERT: D 285 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5228 (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: 0.7647 time to fit residues: 205.4940 Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 340 ASN C 461 GLN D 461 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146864 restraints weight = 15379.555| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.79 r_work: 0.3607 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13320 Z= 0.158 Angle : 0.515 7.623 17944 Z= 0.270 Chirality : 0.041 0.146 1948 Planarity : 0.004 0.031 2276 Dihedral : 5.548 59.798 1768 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.07 % Allowed : 11.14 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1576 helix: 1.64 (0.18), residues: 860 sheet: 1.34 (0.37), residues: 160 loop : -0.65 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 30 TYR 0.011 0.001 TYR A 162 PHE 0.012 0.002 PHE D 80 TRP 0.008 0.001 TRP B 400 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00357 (13320) covalent geometry : angle 0.51499 (17944) hydrogen bonds : bond 0.04361 ( 665) hydrogen bonds : angle 4.11024 ( 1935) *********************** 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 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.378 Fit side-chains REVERT: A 132 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 213 MET cc_start: 0.3346 (ttt) cc_final: 0.2571 (ptp) REVERT: A 285 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: A 336 THR cc_start: 0.7493 (m) cc_final: 0.7230 (t) REVERT: A 358 THR cc_start: 0.7790 (m) cc_final: 0.7323 (t) REVERT: A 372 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7464 (ttm-80) REVERT: B 285 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5495 (mp0) REVERT: B 358 THR cc_start: 0.7854 (m) cc_final: 0.7474 (t) REVERT: B 372 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7460 (ttm-80) REVERT: C 132 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: C 213 MET cc_start: 0.3373 (ttt) cc_final: 0.2440 (ptp) REVERT: C 285 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: C 336 THR cc_start: 0.7419 (m) cc_final: 0.7142 (t) REVERT: C 358 THR cc_start: 0.7825 (m) cc_final: 0.7389 (t) REVERT: C 372 ARG cc_start: 0.7700 (tpp80) cc_final: 0.7494 (ttm-80) REVERT: D 132 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: D 213 MET cc_start: 0.3473 (ttt) cc_final: 0.2403 (ptt) REVERT: D 285 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5404 (mp0) REVERT: D 336 THR cc_start: 0.7474 (m) cc_final: 0.7207 (t) REVERT: D 358 THR cc_start: 0.7844 (m) cc_final: 0.7405 (t) outliers start: 54 outliers final: 17 residues processed: 170 average time/residue: 0.6640 time to fit residues: 121.3977 Evaluate side-chains 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 143 ARG 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 279 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR 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 132 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 285 GLU 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 69 LYS 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 113 optimal weight: 0.0770 chunk 80 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 0.0040 chunk 116 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 410 GLN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148662 restraints weight = 15597.319| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.76 r_work: 0.3654 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1965 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= 0.093 Angle : 0.430 6.916 17944 Z= 0.225 Chirality : 0.039 0.139 1948 Planarity : 0.003 0.035 2276 Dihedral : 5.245 59.454 1768 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.16 % Allowed : 12.65 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1576 helix: 1.77 (0.18), residues: 864 sheet: 1.57 (0.38), residues: 152 loop : -0.56 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.010 0.001 TYR B 162 PHE 0.013 0.001 PHE C 238 TRP 0.008 0.001 TRP B 135 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00199 (13320) covalent geometry : angle 0.43001 (17944) hydrogen bonds : bond 0.03530 ( 665) hydrogen bonds : angle 3.81801 ( 1935) *********************** 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 206 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.559 Fit side-chains REVERT: A 213 MET cc_start: 0.3405 (ttt) cc_final: 0.2337 (ptt) REVERT: A 285 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5374 (mp0) REVERT: A 358 THR cc_start: 0.7852 (m) cc_final: 0.7328 (t) REVERT: A 372 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7443 (ttm-80) REVERT: B 98 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 129 ASN cc_start: 0.7906 (m-40) cc_final: 0.7691 (m-40) REVERT: B 285 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5487 (mp0) REVERT: B 358 THR cc_start: 0.7791 (m) cc_final: 0.7393 (t) REVERT: C 213 MET cc_start: 0.3213 (ttt) cc_final: 0.2375 (ptp) REVERT: C 285 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: C 336 THR cc_start: 0.7274 (m) cc_final: 0.7060 (t) REVERT: C 358 THR cc_start: 0.7839 (m) cc_final: 0.7376 (t) REVERT: C 372 ARG cc_start: 0.7658 (tpp80) cc_final: 0.7456 (ttm-80) REVERT: D 213 MET cc_start: 0.3451 (ttt) cc_final: 0.2441 (ptt) REVERT: D 285 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5380 (mp0) REVERT: D 336 THR cc_start: 0.7334 (m) cc_final: 0.7127 (t) REVERT: D 358 THR cc_start: 0.7810 (m) cc_final: 0.7352 (t) outliers start: 42 outliers final: 8 residues processed: 177 average time/residue: 0.6862 time to fit residues: 130.9180 Evaluate side-chains 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 282 LEU 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 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 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144570 restraints weight = 15606.166| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.78 r_work: 0.3604 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13320 Z= 0.167 Angle : 0.518 7.366 17944 Z= 0.272 Chirality : 0.041 0.145 1948 Planarity : 0.004 0.034 2276 Dihedral : 5.485 57.204 1768 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.29 % Allowed : 12.35 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1576 helix: 1.49 (0.18), residues: 864 sheet: 0.92 (0.38), residues: 164 loop : -0.74 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 390 TYR 0.011 0.001 TYR D 408 PHE 0.015 0.002 PHE C 238 TRP 0.010 0.001 TRP A 400 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00380 (13320) covalent geometry : angle 0.51798 (17944) hydrogen bonds : bond 0.04433 ( 665) hydrogen bonds : angle 4.16159 ( 1935) *********************** 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 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.481 Fit side-chains REVERT: A 21 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6359 (pp20) REVERT: A 129 ASN cc_start: 0.7923 (m-40) cc_final: 0.7680 (m-40) REVERT: A 132 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 167 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (mmt180) REVERT: A 213 MET cc_start: 0.3324 (ttt) cc_final: 0.2349 (ptt) REVERT: A 285 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: A 333 LYS cc_start: 0.7159 (tmmt) cc_final: 0.6949 (tmmt) REVERT: A 358 THR cc_start: 0.7834 (m) cc_final: 0.7281 (t) REVERT: A 372 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7438 (ttm-80) REVERT: B 21 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6382 (pp20) REVERT: B 129 ASN cc_start: 0.7935 (m-40) cc_final: 0.7704 (m-40) REVERT: B 132 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: B 285 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5723 (mp0) REVERT: B 358 THR cc_start: 0.7824 (m) cc_final: 0.7391 (t) REVERT: C 132 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 213 MET cc_start: 0.3270 (ttt) cc_final: 0.2314 (ptt) REVERT: C 285 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: C 372 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7429 (ttm-80) REVERT: D 132 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: D 213 MET cc_start: 0.3324 (ttt) cc_final: 0.2336 (ptt) REVERT: D 285 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5668 (mp0) REVERT: D 358 THR cc_start: 0.7860 (m) cc_final: 0.7381 (t) REVERT: D 372 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7287 (mtm-85) outliers start: 57 outliers final: 20 residues processed: 172 average time/residue: 0.6222 time to fit residues: 116.3389 Evaluate side-chains 161 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU 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 282 LEU Chi-restraints excluded: chain A residue 285 GLU 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 132 GLU 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 430 ASN Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 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 402 GLU Chi-restraints excluded: chain C residue 430 ASN 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 143 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 65 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141767 restraints weight = 15726.852| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.77 r_work: 0.3569 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13320 Z= 0.280 Angle : 0.651 8.267 17944 Z= 0.343 Chirality : 0.046 0.147 1948 Planarity : 0.005 0.037 2276 Dihedral : 5.917 51.736 1768 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.44 % Allowed : 13.55 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1576 helix: 0.79 (0.17), residues: 868 sheet: 0.54 (0.36), residues: 172 loop : -0.88 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.016 0.002 TYR A 408 PHE 0.021 0.003 PHE C 80 TRP 0.015 0.002 TRP A 400 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00647 (13320) covalent geometry : angle 0.65057 (17944) hydrogen bonds : bond 0.05332 ( 665) hydrogen bonds : angle 4.71044 ( 1935) *********************** 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 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 0.583 Fit side-chains REVERT: A 167 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7816 (mmm160) REVERT: A 333 LYS cc_start: 0.7245 (tmmt) cc_final: 0.6959 (tmmt) REVERT: A 334 LYS cc_start: 0.6778 (ptpt) cc_final: 0.6547 (pttt) REVERT: A 358 THR cc_start: 0.7926 (m) cc_final: 0.7434 (t) REVERT: A 372 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7416 (ttm-80) REVERT: A 410 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: B 132 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: B 279 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (tt) REVERT: B 358 THR cc_start: 0.7867 (m) cc_final: 0.7419 (t) REVERT: B 410 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: C 132 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: C 133 HIS cc_start: 0.7615 (t70) cc_final: 0.7313 (t-170) REVERT: C 167 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: C 285 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6257 (pp20) REVERT: C 372 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7441 (ttm-80) REVERT: C 410 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: D 167 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7900 (mmp80) REVERT: D 285 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: D 358 THR cc_start: 0.7921 (m) cc_final: 0.7469 (t) REVERT: D 372 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7290 (mtm-85) outliers start: 59 outliers final: 27 residues processed: 166 average time/residue: 0.6607 time to fit residues: 118.6580 Evaluate side-chains 154 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 338 LYS 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 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 430 ASN 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 143 ARG Chi-restraints excluded: chain C residue 167 ARG 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 410 GLN Chi-restraints excluded: chain C residue 430 ASN 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 143 ARG Chi-restraints excluded: chain D residue 167 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 124 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 60 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.180649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145910 restraints weight = 15585.154| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.77 r_work: 0.3624 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13320 Z= 0.115 Angle : 0.468 7.036 17944 Z= 0.248 Chirality : 0.040 0.134 1948 Planarity : 0.004 0.036 2276 Dihedral : 5.419 51.744 1768 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.39 % Allowed : 15.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1576 helix: 1.36 (0.18), residues: 868 sheet: 1.16 (0.39), residues: 156 loop : -0.68 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 30 TYR 0.007 0.001 TYR C 325 PHE 0.014 0.001 PHE B 15 TRP 0.010 0.001 TRP A 135 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00252 (13320) covalent geometry : angle 0.46833 (17944) hydrogen bonds : bond 0.03885 ( 665) hydrogen bonds : angle 4.15795 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.510 Fit side-chains REVERT: A 213 MET cc_start: 0.3195 (ttt) cc_final: 0.2441 (ptp) REVERT: A 285 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: A 333 LYS cc_start: 0.7193 (tmmt) cc_final: 0.6885 (tmmt) REVERT: A 334 LYS cc_start: 0.6726 (ptpt) cc_final: 0.6494 (pttt) REVERT: A 358 THR cc_start: 0.7850 (m) cc_final: 0.7346 (t) REVERT: A 372 ARG cc_start: 0.7562 (tpp80) cc_final: 0.7349 (ttm-80) REVERT: B 129 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: B 132 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: B 285 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: B 358 THR cc_start: 0.7867 (m) cc_final: 0.7381 (t) REVERT: B 410 GLN cc_start: 0.7209 (pt0) cc_final: 0.6618 (tt0) REVERT: C 213 MET cc_start: 0.3188 (ttt) cc_final: 0.2408 (ptt) REVERT: C 285 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: C 372 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7350 (ttm-80) REVERT: D 213 MET cc_start: 0.3167 (ttt) cc_final: 0.2314 (ptt) REVERT: D 285 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5619 (mp0) REVERT: D 358 THR cc_start: 0.7863 (m) cc_final: 0.7418 (t) outliers start: 45 outliers final: 17 residues processed: 156 average time/residue: 0.6167 time to fit residues: 104.6775 Evaluate side-chains 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR 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 430 ASN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 132 GLU 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 430 ASN Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR 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 430 ASN Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 285 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 73 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.180899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146269 restraints weight = 15698.278| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.77 r_work: 0.3629 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2531 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= 0.113 Angle : 0.463 6.955 17944 Z= 0.244 Chirality : 0.040 0.138 1948 Planarity : 0.003 0.037 2276 Dihedral : 5.302 51.882 1768 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.94 % Allowed : 16.49 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1576 helix: 1.46 (0.18), residues: 868 sheet: 1.30 (0.39), residues: 156 loop : -0.66 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 390 TYR 0.008 0.001 TYR C 325 PHE 0.012 0.001 PHE C 15 TRP 0.011 0.001 TRP A 400 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00251 (13320) covalent geometry : angle 0.46298 (17944) hydrogen bonds : bond 0.03782 ( 665) hydrogen bonds : angle 4.05899 ( 1935) *********************** 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 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.490 Fit side-chains REVERT: A 213 MET cc_start: 0.3179 (ttt) cc_final: 0.2481 (ptp) REVERT: A 285 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5735 (mp0) REVERT: A 358 THR cc_start: 0.7838 (m) cc_final: 0.7262 (t) REVERT: A 372 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7267 (ttm-80) REVERT: B 129 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7659 (m-40) REVERT: B 285 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5760 (mp0) REVERT: B 358 THR cc_start: 0.7873 (m) cc_final: 0.7394 (t) REVERT: C 213 MET cc_start: 0.3108 (ttt) cc_final: 0.2536 (ptp) REVERT: C 285 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: D 213 MET cc_start: 0.3165 (ttt) cc_final: 0.2274 (ptt) REVERT: D 285 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5581 (mp0) REVERT: D 358 THR cc_start: 0.7866 (m) cc_final: 0.7377 (t) REVERT: D 410 GLN cc_start: 0.7260 (pt0) cc_final: 0.6771 (tt0) outliers start: 39 outliers final: 20 residues processed: 154 average time/residue: 0.5891 time to fit residues: 99.0434 Evaluate side-chains 153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 75 THR 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 430 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 129 ASN 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 430 ASN Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR 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 430 ASN Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 285 GLU 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 130 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 153 optimal weight: 3.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.179724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.144938 restraints weight = 15472.760| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.76 r_work: 0.3609 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13320 Z= 0.150 Angle : 0.504 7.225 17944 Z= 0.266 Chirality : 0.041 0.139 1948 Planarity : 0.004 0.037 2276 Dihedral : 5.403 50.630 1768 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.16 % Allowed : 15.96 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1576 helix: 1.38 (0.18), residues: 864 sheet: 1.00 (0.39), residues: 164 loop : -0.76 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 390 TYR 0.008 0.001 TYR D 408 PHE 0.018 0.002 PHE C 15 TRP 0.015 0.002 TRP A 400 HIS 0.004 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00342 (13320) covalent geometry : angle 0.50448 (17944) hydrogen bonds : bond 0.04183 ( 665) hydrogen bonds : angle 4.23470 ( 1935) *********************** 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 166 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.382 Fit side-chains REVERT: A 285 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6150 (pp20) REVERT: A 333 LYS cc_start: 0.7157 (tmmt) cc_final: 0.6857 (tmmt) REVERT: A 372 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7358 (ttm-80) REVERT: B 129 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: B 132 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: B 285 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5747 (mp0) REVERT: C 285 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5745 (mp0) REVERT: D 285 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5609 (mp0) REVERT: D 358 THR cc_start: 0.7859 (m) cc_final: 0.7358 (t) REVERT: D 410 GLN cc_start: 0.7345 (pt0) cc_final: 0.6883 (tt0) outliers start: 42 outliers final: 21 residues processed: 147 average time/residue: 0.6089 time to fit residues: 97.2785 Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE 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 129 ASN Chi-restraints excluded: chain B residue 132 GLU 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 430 ASN Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 THR 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 430 ASN 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 285 GLU 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 77 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.179938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145032 restraints weight = 15668.966| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.78 r_work: 0.3613 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13320 Z= 0.146 Angle : 0.498 7.314 17944 Z= 0.263 Chirality : 0.041 0.138 1948 Planarity : 0.004 0.037 2276 Dihedral : 5.386 49.773 1768 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.56 % Allowed : 16.79 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1576 helix: 1.37 (0.18), residues: 864 sheet: 1.29 (0.40), residues: 156 loop : -0.69 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.008 0.001 TYR B 408 PHE 0.018 0.002 PHE A 15 TRP 0.018 0.002 TRP A 400 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00332 (13320) covalent geometry : angle 0.49820 (17944) hydrogen bonds : bond 0.04163 ( 665) hydrogen bonds : angle 4.26410 ( 1935) *********************** 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 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.529 Fit side-chains REVERT: A 285 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6183 (pp20) REVERT: A 333 LYS cc_start: 0.7205 (tmmt) cc_final: 0.6901 (tmmt) REVERT: A 358 THR cc_start: 0.7868 (m) cc_final: 0.7290 (t) REVERT: B 129 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7686 (m-40) REVERT: B 132 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: B 285 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6183 (pp20) REVERT: C 285 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6165 (pp20) REVERT: D 285 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5611 (mp0) REVERT: D 358 THR cc_start: 0.7869 (m) cc_final: 0.7367 (t) REVERT: D 410 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6946 (tt0) outliers start: 34 outliers final: 22 residues processed: 133 average time/residue: 0.6061 time to fit residues: 87.5373 Evaluate side-chains 139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 291 ILE 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 129 ASN Chi-restraints excluded: chain B residue 132 GLU 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 430 ASN 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 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 430 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.179073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144224 restraints weight = 15652.893| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.77 r_work: 0.3601 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13320 Z= 0.171 Angle : 0.531 7.649 17944 Z= 0.280 Chirality : 0.042 0.140 1948 Planarity : 0.004 0.037 2276 Dihedral : 5.506 47.465 1768 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.48 % Allowed : 16.94 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1576 helix: 1.27 (0.18), residues: 864 sheet: 0.86 (0.38), residues: 172 loop : -0.77 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 390 TYR 0.010 0.001 TYR B 408 PHE 0.021 0.002 PHE C 15 TRP 0.019 0.002 TRP D 400 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00392 (13320) covalent geometry : angle 0.53068 (17944) hydrogen bonds : bond 0.04435 ( 665) hydrogen bonds : angle 4.40291 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.505 Fit side-chains REVERT: A 333 LYS cc_start: 0.7217 (tmmt) cc_final: 0.6912 (tmmt) REVERT: A 358 THR cc_start: 0.7891 (m) cc_final: 0.7342 (t) REVERT: B 129 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: B 132 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 358 THR cc_start: 0.7922 (m) cc_final: 0.7715 (m) REVERT: D 358 THR cc_start: 0.7911 (m) cc_final: 0.7437 (t) REVERT: D 372 ARG cc_start: 0.7734 (tpp80) cc_final: 0.7275 (mtm-85) REVERT: D 410 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6932 (tt0) outliers start: 33 outliers final: 25 residues processed: 128 average time/residue: 0.6347 time to fit residues: 88.2801 Evaluate side-chains 132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 LEU Chi-restraints excluded: chain A residue 285 GLU 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 129 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 430 ASN 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 282 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 430 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.180259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145326 restraints weight = 15622.921| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.78 r_work: 0.3617 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13320 Z= 0.135 Angle : 0.499 7.202 17944 Z= 0.263 Chirality : 0.041 0.137 1948 Planarity : 0.004 0.036 2276 Dihedral : 5.384 48.480 1768 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.26 % Allowed : 17.55 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1576 helix: 1.33 (0.18), residues: 868 sheet: 1.36 (0.40), residues: 156 loop : -0.65 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 390 TYR 0.006 0.001 TYR B 408 PHE 0.020 0.002 PHE B 15 TRP 0.016 0.002 TRP D 400 HIS 0.006 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00305 (13320) covalent geometry : angle 0.49902 (17944) hydrogen bonds : bond 0.04071 ( 665) hydrogen bonds : angle 4.28973 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.00 seconds wall clock time: 83 minutes 26.28 seconds (5006.28 seconds total)