Starting phenix.real_space_refine on Sat Jun 14 01:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.map" model { file = "/net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e76_27936/06_2025/8e76_27936.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10208 2.51 5 N 2724 2.21 5 O 2912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15928 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3982 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Restraints were copied for chains: C, B, D Time building chain proxies: 8.40, per 1000 atoms: 0.53 Number of scatterers: 15928 At special positions: 0 Unit cell: (132.08, 135.2, 78, 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 84 16.00 O 2912 8.00 N 2724 7.00 C 10208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3728 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 54.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.184A pdb=" N THR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 7 " --> pdb=" O TYR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 80 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 7 " --> pdb=" O TYR B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 80 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.598A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 207 through 224 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 291 through 307 removed outlier: 4.161A pdb=" N GLY B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.883A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 511 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR C 6 " --> pdb=" O GLY C 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 7 " --> pdb=" O TYR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 80 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 154 through 169 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 207 through 224 Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 511 Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR D 6 " --> pdb=" O GLY D 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 7 " --> pdb=" O TYR D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 80 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 207 through 224 Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 492 through 511 Processing helix chain 'D' and resid 522 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 7.075A pdb=" N PHE A 35 " --> pdb=" O GLN B 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU A 110 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP A 181 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 112 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.557A pdb=" N PHE A 284 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY A 437 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 419 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU B 110 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP B 181 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 112 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.557A pdb=" N PHE B 284 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY B 437 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 419 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.075A pdb=" N PHE C 35 " --> pdb=" O GLN D 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.384A pdb=" N LEU C 110 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 181 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 112 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.558A pdb=" N PHE C 284 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY C 437 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 419 " --> pdb=" O GLY C 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AB2, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU D 110 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP D 181 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 112 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.558A pdb=" N PHE D 284 " --> pdb=" O TRP D 319 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY D 437 " --> pdb=" O PHE D 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 419 " --> pdb=" O GLY D 437 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5182 1.34 - 1.45: 2603 1.45 - 1.57: 8359 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 16276 Sorted by residual: bond pdb=" C ASN A 395 " pdb=" N PRO A 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.56e+00 bond pdb=" C ASN C 395 " pdb=" N PRO C 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.54e+00 bond pdb=" C ASN D 395 " pdb=" N PRO D 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.45e+00 bond pdb=" C ASN B 395 " pdb=" N PRO B 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.43e+00 bond pdb=" CB ARG D 247 " pdb=" CG ARG D 247 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.30e+00 ... (remaining 16271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21363 1.82 - 3.64: 588 3.64 - 5.47: 77 5.47 - 7.29: 16 7.29 - 9.11: 4 Bond angle restraints: 22048 Sorted by residual: angle pdb=" N GLU A 405 " pdb=" CA GLU A 405 " pdb=" C GLU A 405 " ideal model delta sigma weight residual 113.43 106.93 6.50 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU B 405 " pdb=" CA GLU B 405 " pdb=" C GLU B 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU D 405 " pdb=" CA GLU D 405 " pdb=" C GLU D 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU C 405 " pdb=" CA GLU C 405 " pdb=" C GLU C 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.65e+01 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 113.43 109.30 4.13 1.26e+00 6.30e-01 1.07e+01 ... (remaining 22043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 8613 16.18 - 32.35: 871 32.35 - 48.53: 192 48.53 - 64.71: 44 64.71 - 80.88: 24 Dihedral angle restraints: 9744 sinusoidal: 3912 harmonic: 5832 Sorted by residual: dihedral pdb=" CA CYS D 151 " pdb=" C CYS D 151 " pdb=" N TYR D 152 " pdb=" CA TYR D 152 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA CYS A 151 " pdb=" C CYS A 151 " pdb=" N TYR A 152 " pdb=" CA TYR A 152 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA CYS B 151 " pdb=" C CYS B 151 " pdb=" N TYR B 152 " pdb=" CA TYR B 152 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1247 0.032 - 0.064: 843 0.064 - 0.095: 242 0.095 - 0.127: 112 0.127 - 0.159: 20 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PHE B 445 " pdb=" N PHE B 445 " pdb=" C PHE B 445 " pdb=" CB PHE B 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE D 445 " pdb=" N PHE D 445 " pdb=" C PHE D 445 " pdb=" CB PHE D 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA PHE A 445 " pdb=" N PHE A 445 " pdb=" C PHE A 445 " pdb=" CB PHE A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 2461 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 309 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 310 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 310 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 310 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 309 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 310 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 309 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 310 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 310 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 310 " -0.022 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 499 2.70 - 3.25: 16453 3.25 - 3.80: 28301 3.80 - 4.35: 37030 4.35 - 4.90: 58382 Nonbonded interactions: 140665 Sorted by model distance: nonbonded pdb=" O GLY D 150 " pdb=" OH TYR D 195 " model vdw 2.155 3.040 nonbonded pdb=" O GLY B 150 " pdb=" OH TYR B 195 " model vdw 2.155 3.040 nonbonded pdb=" O GLY C 150 " pdb=" OH TYR C 195 " model vdw 2.156 3.040 nonbonded pdb=" O GLY A 150 " pdb=" OH TYR A 195 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASP A 213 " pdb=" OH TYR A 246 " model vdw 2.192 3.040 ... (remaining 140660 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.380 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:54.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.007 0.049 16276 Z= 0.317 Angle : 0.722 9.110 22048 Z= 0.396 Chirality : 0.047 0.159 2464 Planarity : 0.004 0.041 2844 Dihedral : 14.221 80.882 6016 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2000 helix: -1.20 (0.15), residues: 944 sheet: -0.49 (0.39), residues: 192 loop : -2.03 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 127 HIS 0.004 0.001 HIS B 511 PHE 0.019 0.002 PHE D 35 TYR 0.015 0.002 TYR A 74 ARG 0.006 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.16575 ( 690) hydrogen bonds : angle 8.23506 ( 2010) covalent geometry : bond 0.00747 (16276) covalent geometry : angle 0.72236 (22048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.4035 (tpp) cc_final: 0.3753 (tpp) REVERT: B 269 LEU cc_start: 0.7271 (mt) cc_final: 0.7051 (mt) REVERT: C 63 MET cc_start: 0.5901 (mmp) cc_final: 0.5471 (mmt) outliers start: 0 outliers final: 2 residues processed: 329 average time/residue: 1.5211 time to fit residues: 568.3137 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain D residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 41 GLN A 66 GLN A 115 HIS A 174 GLN A 281 ASN A 459 HIS A 480 HIS B 41 GLN B 66 GLN B 115 HIS B 174 GLN B 217 GLN B 281 ASN B 459 HIS B 480 HIS C 41 GLN C 66 GLN C 174 GLN C 281 ASN C 459 HIS D 28 HIS D 41 GLN D 66 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 174 GLN D 459 HIS ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.087363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069595 restraints weight = 45920.981| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.52 r_work: 0.3119 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16276 Z= 0.186 Angle : 0.701 9.868 22048 Z= 0.361 Chirality : 0.044 0.191 2464 Planarity : 0.005 0.054 2844 Dihedral : 5.115 31.146 2212 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.11 % Allowed : 14.34 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2000 helix: 0.05 (0.16), residues: 952 sheet: -0.17 (0.41), residues: 188 loop : -1.63 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 319 HIS 0.013 0.001 HIS B 298 PHE 0.029 0.002 PHE D 526 TYR 0.025 0.002 TYR D 487 ARG 0.011 0.001 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 690) hydrogen bonds : angle 5.63834 ( 2010) covalent geometry : bond 0.00419 (16276) covalent geometry : angle 0.70098 (22048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8987 (mtm) cc_final: 0.8782 (mtm) REVERT: A 100 TYR cc_start: 0.6530 (t80) cc_final: 0.6295 (t80) REVERT: A 320 MET cc_start: 0.7307 (mtt) cc_final: 0.6908 (mtt) REVERT: A 407 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 302 MET cc_start: 0.9144 (mtp) cc_final: 0.8871 (mtp) REVERT: B 406 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6023 (mttt) REVERT: B 408 TYR cc_start: 0.7099 (m-80) cc_final: 0.6849 (m-80) REVERT: B 490 LEU cc_start: 0.8759 (mt) cc_final: 0.8493 (mt) REVERT: C 63 MET cc_start: 0.8983 (mmp) cc_final: 0.8637 (mmp) REVERT: C 154 MET cc_start: 0.8520 (tpp) cc_final: 0.8273 (tpt) REVERT: C 282 HIS cc_start: 0.6664 (m90) cc_final: 0.6332 (m90) REVERT: C 468 THR cc_start: 0.8962 (p) cc_final: 0.8738 (p) REVERT: D 89 TYR cc_start: 0.5677 (t80) cc_final: 0.5320 (t80) REVERT: D 260 THR cc_start: 0.9307 (m) cc_final: 0.9023 (p) REVERT: D 294 MET cc_start: 0.8854 (mmm) cc_final: 0.8615 (mmm) REVERT: D 304 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8752 (mm) outliers start: 36 outliers final: 9 residues processed: 216 average time/residue: 0.9214 time to fit residues: 231.6502 Evaluate side-chains 176 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 8 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.086393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068645 restraints weight = 45574.820| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.49 r_work: 0.3101 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16276 Z= 0.123 Angle : 0.610 8.780 22048 Z= 0.314 Chirality : 0.043 0.263 2464 Planarity : 0.004 0.054 2844 Dihedral : 4.712 20.526 2208 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.52 % Allowed : 14.64 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2000 helix: 0.30 (0.16), residues: 964 sheet: -0.50 (0.42), residues: 164 loop : -1.44 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 319 HIS 0.010 0.001 HIS B 298 PHE 0.022 0.002 PHE D 526 TYR 0.024 0.001 TYR D 164 ARG 0.006 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 690) hydrogen bonds : angle 5.18235 ( 2010) covalent geometry : bond 0.00281 (16276) covalent geometry : angle 0.60972 (22048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9068 (mtm) cc_final: 0.8846 (mtm) REVERT: A 100 TYR cc_start: 0.7060 (t80) cc_final: 0.6292 (t80) REVERT: A 294 MET cc_start: 0.9129 (mmm) cc_final: 0.8928 (mmm) REVERT: A 298 HIS cc_start: 0.9363 (m-70) cc_final: 0.9089 (m-70) REVERT: B 302 MET cc_start: 0.9158 (mtp) cc_final: 0.8935 (mtp) REVERT: B 395 ASN cc_start: 0.8850 (p0) cc_final: 0.8532 (p0) REVERT: B 406 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6475 (mttt) REVERT: B 490 LEU cc_start: 0.8996 (mt) cc_final: 0.8785 (tp) REVERT: C 63 MET cc_start: 0.9096 (mmp) cc_final: 0.8723 (mmt) REVERT: C 92 THR cc_start: 0.8560 (m) cc_final: 0.8229 (p) REVERT: C 154 MET cc_start: 0.8472 (tpp) cc_final: 0.8266 (tpt) REVERT: C 282 HIS cc_start: 0.6755 (m90) cc_final: 0.6459 (m90) REVERT: C 302 MET cc_start: 0.8019 (mtm) cc_final: 0.7640 (mtp) REVERT: C 320 MET cc_start: 0.7840 (pmm) cc_final: 0.7350 (mtt) REVERT: D 67 ASP cc_start: 0.8254 (p0) cc_final: 0.7158 (p0) REVERT: D 100 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: D 260 THR cc_start: 0.9378 (m) cc_final: 0.9095 (p) REVERT: D 294 MET cc_start: 0.8839 (mmm) cc_final: 0.8578 (mmm) REVERT: D 298 HIS cc_start: 0.9034 (t-90) cc_final: 0.8620 (m-70) REVERT: D 304 LEU cc_start: 0.8989 (mm) cc_final: 0.8748 (mm) REVERT: D 320 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.5715 (pp-130) REVERT: D 441 ASN cc_start: 0.8666 (m-40) cc_final: 0.8338 (t0) outliers start: 43 outliers final: 6 residues processed: 207 average time/residue: 0.7988 time to fit residues: 194.6017 Evaluate side-chains 174 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054463 restraints weight = 46408.610| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.29 r_work: 0.2768 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16276 Z= 0.224 Angle : 0.679 7.916 22048 Z= 0.356 Chirality : 0.045 0.204 2464 Planarity : 0.005 0.071 2844 Dihedral : 4.643 22.856 2208 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.63 % Allowed : 15.46 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 2000 helix: 0.41 (0.17), residues: 968 sheet: -0.35 (0.42), residues: 168 loop : -1.17 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 319 HIS 0.048 0.002 HIS C 480 PHE 0.041 0.002 PHE A 434 TYR 0.017 0.002 TYR A 164 ARG 0.014 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 690) hydrogen bonds : angle 5.17960 ( 2010) covalent geometry : bond 0.00507 (16276) covalent geometry : angle 0.67887 (22048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9363 (mtm) cc_final: 0.9084 (mtm) REVERT: A 294 MET cc_start: 0.9291 (mmm) cc_final: 0.8960 (mmm) REVERT: A 305 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8920 (mm-30) REVERT: A 416 ILE cc_start: 0.8888 (mt) cc_final: 0.8628 (mm) REVERT: B 294 MET cc_start: 0.8548 (mmm) cc_final: 0.8307 (mpp) REVERT: B 302 MET cc_start: 0.9277 (mtp) cc_final: 0.9022 (mtp) REVERT: B 408 TYR cc_start: 0.7043 (m-80) cc_final: 0.6790 (m-80) REVERT: B 416 ILE cc_start: 0.8308 (mt) cc_final: 0.8017 (mm) REVERT: C 80 ASP cc_start: 0.8676 (t0) cc_final: 0.8283 (t0) REVERT: C 282 HIS cc_start: 0.7183 (m90) cc_final: 0.6942 (m90) REVERT: C 294 MET cc_start: 0.9073 (tpp) cc_final: 0.8826 (mmm) REVERT: C 302 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8526 (mtp) REVERT: C 405 GLU cc_start: 0.8357 (tt0) cc_final: 0.7451 (mm-30) REVERT: C 440 ASN cc_start: 0.8898 (t0) cc_final: 0.8608 (t0) REVERT: C 480 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8546 (t-90) REVERT: D 100 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: D 294 MET cc_start: 0.9157 (mmm) cc_final: 0.8926 (mmm) REVERT: D 305 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8447 (mm-30) REVERT: D 395 ASN cc_start: 0.8993 (m-40) cc_final: 0.8367 (p0) REVERT: D 524 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (tm-30) outliers start: 45 outliers final: 10 residues processed: 173 average time/residue: 1.0243 time to fit residues: 203.8745 Evaluate side-chains 137 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054338 restraints weight = 46722.314| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.29 r_work: 0.2762 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16276 Z= 0.134 Angle : 0.580 10.315 22048 Z= 0.298 Chirality : 0.043 0.231 2464 Planarity : 0.004 0.048 2844 Dihedral : 4.422 19.299 2208 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.58 % Allowed : 17.04 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2000 helix: 0.62 (0.17), residues: 968 sheet: -0.49 (0.42), residues: 168 loop : -1.13 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 319 HIS 0.007 0.001 HIS C 480 PHE 0.023 0.002 PHE D 445 TYR 0.013 0.001 TYR D 487 ARG 0.004 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 690) hydrogen bonds : angle 4.93412 ( 2010) covalent geometry : bond 0.00312 (16276) covalent geometry : angle 0.57957 (22048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9424 (mtm) cc_final: 0.9144 (mtm) REVERT: A 67 ASP cc_start: 0.8879 (p0) cc_final: 0.8671 (p0) REVERT: A 305 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8946 (mm-30) REVERT: A 416 ILE cc_start: 0.9023 (mt) cc_final: 0.8768 (mm) REVERT: B 294 MET cc_start: 0.8644 (mmm) cc_final: 0.8320 (mpp) REVERT: B 302 MET cc_start: 0.9291 (mtp) cc_final: 0.9032 (mtp) REVERT: B 408 TYR cc_start: 0.6997 (m-80) cc_final: 0.6647 (m-80) REVERT: C 80 ASP cc_start: 0.8652 (t0) cc_final: 0.8241 (t0) REVERT: C 100 TYR cc_start: 0.6980 (t80) cc_final: 0.6750 (t80) REVERT: C 294 MET cc_start: 0.8915 (tpp) cc_final: 0.8706 (mmm) REVERT: C 302 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: C 405 GLU cc_start: 0.8360 (tt0) cc_final: 0.7413 (mm-30) REVERT: C 440 ASN cc_start: 0.9041 (t0) cc_final: 0.8768 (t160) REVERT: D 100 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: D 294 MET cc_start: 0.9061 (mmm) cc_final: 0.8847 (mmm) REVERT: D 305 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: D 395 ASN cc_start: 0.8993 (m-40) cc_final: 0.8373 (p0) REVERT: D 524 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8577 (tm-30) outliers start: 27 outliers final: 6 residues processed: 152 average time/residue: 1.1164 time to fit residues: 193.4413 Evaluate side-chains 129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054476 restraints weight = 46239.170| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.24 r_work: 0.2774 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16276 Z= 0.118 Angle : 0.601 18.131 22048 Z= 0.301 Chirality : 0.043 0.249 2464 Planarity : 0.004 0.046 2844 Dihedral : 4.307 19.165 2208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.23 % Allowed : 17.51 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2000 helix: 0.69 (0.17), residues: 968 sheet: -0.47 (0.42), residues: 168 loop : -1.04 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 319 HIS 0.006 0.001 HIS B 298 PHE 0.022 0.001 PHE D 445 TYR 0.015 0.001 TYR B 208 ARG 0.008 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 690) hydrogen bonds : angle 4.85970 ( 2010) covalent geometry : bond 0.00275 (16276) covalent geometry : angle 0.60084 (22048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9391 (mtm) cc_final: 0.9111 (mtm) REVERT: A 305 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8937 (mm-30) REVERT: A 416 ILE cc_start: 0.9014 (mt) cc_final: 0.8769 (mm) REVERT: B 294 MET cc_start: 0.8613 (mmm) cc_final: 0.8303 (mpp) REVERT: B 302 MET cc_start: 0.9295 (mtp) cc_final: 0.9009 (mtp) REVERT: C 80 ASP cc_start: 0.8726 (t0) cc_final: 0.8353 (t0) REVERT: C 100 TYR cc_start: 0.7166 (t80) cc_final: 0.6935 (t80) REVERT: C 302 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: C 405 GLU cc_start: 0.8395 (tt0) cc_final: 0.7444 (mm-30) REVERT: C 440 ASN cc_start: 0.9067 (t0) cc_final: 0.8787 (t160) REVERT: D 100 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: D 305 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: D 320 MET cc_start: 0.7532 (mpp) cc_final: 0.6016 (pp-130) REVERT: D 395 ASN cc_start: 0.8953 (m-40) cc_final: 0.8380 (p0) REVERT: D 524 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: D 537 ASP cc_start: 0.8503 (t0) cc_final: 0.8055 (t0) outliers start: 21 outliers final: 7 residues processed: 145 average time/residue: 0.9921 time to fit residues: 164.9155 Evaluate side-chains 131 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 ASN C 28 HIS ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047580 restraints weight = 47389.606| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.19 r_work: 0.2589 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16276 Z= 0.307 Angle : 0.716 11.658 22048 Z= 0.362 Chirality : 0.047 0.264 2464 Planarity : 0.005 0.046 2844 Dihedral : 4.569 20.201 2208 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.35 % Allowed : 17.92 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 2000 helix: 0.77 (0.17), residues: 964 sheet: -0.45 (0.43), residues: 168 loop : -0.92 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 319 HIS 0.007 0.001 HIS A 28 PHE 0.017 0.002 PHE B 104 TYR 0.022 0.002 TYR B 74 ARG 0.009 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 690) hydrogen bonds : angle 5.16029 ( 2010) covalent geometry : bond 0.00696 (16276) covalent geometry : angle 0.71613 (22048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.9444 (mtm) cc_final: 0.9112 (mtm) REVERT: A 305 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9043 (mm-30) REVERT: A 551 MET cc_start: 0.8958 (ttm) cc_final: 0.8632 (ttm) REVERT: B 294 MET cc_start: 0.8832 (mmm) cc_final: 0.8578 (mmm) REVERT: B 302 MET cc_start: 0.9474 (mtp) cc_final: 0.9203 (mtp) REVERT: B 416 ILE cc_start: 0.9133 (mt) cc_final: 0.8864 (mm) REVERT: C 15 MET cc_start: 0.9343 (mtm) cc_final: 0.9137 (mtt) REVERT: C 80 ASP cc_start: 0.8978 (t0) cc_final: 0.8047 (t0) REVERT: C 302 MET cc_start: 0.9344 (mtm) cc_final: 0.9041 (mtp) REVERT: C 405 GLU cc_start: 0.8791 (tt0) cc_final: 0.7914 (mm-30) REVERT: C 462 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8955 (m-30) REVERT: D 100 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: D 305 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8552 (mm-30) REVERT: D 395 ASN cc_start: 0.8964 (m-40) cc_final: 0.8485 (p0) REVERT: D 524 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8673 (tm-30) outliers start: 23 outliers final: 7 residues processed: 129 average time/residue: 1.0011 time to fit residues: 148.0392 Evaluate side-chains 117 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 128 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 93 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049872 restraints weight = 46023.983| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.09 r_work: 0.2651 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16276 Z= 0.143 Angle : 0.620 13.004 22048 Z= 0.311 Chirality : 0.043 0.246 2464 Planarity : 0.004 0.044 2844 Dihedral : 4.406 18.629 2208 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.82 % Allowed : 18.62 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2000 helix: 0.85 (0.17), residues: 960 sheet: -0.49 (0.43), residues: 168 loop : -0.94 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 319 HIS 0.004 0.001 HIS B 298 PHE 0.021 0.002 PHE B 445 TYR 0.014 0.001 TYR D 487 ARG 0.006 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 690) hydrogen bonds : angle 4.93005 ( 2010) covalent geometry : bond 0.00336 (16276) covalent geometry : angle 0.62021 (22048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 2.960 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.9434 (mtm) cc_final: 0.9091 (mtm) REVERT: A 305 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9035 (mm-30) REVERT: A 416 ILE cc_start: 0.9160 (mt) cc_final: 0.8892 (mm) REVERT: A 551 MET cc_start: 0.8651 (ttm) cc_final: 0.8366 (ttm) REVERT: B 63 MET cc_start: 0.9027 (mmp) cc_final: 0.8761 (mmp) REVERT: B 294 MET cc_start: 0.8784 (mmm) cc_final: 0.8528 (mmm) REVERT: B 302 MET cc_start: 0.9431 (mtp) cc_final: 0.9154 (mtp) REVERT: B 416 ILE cc_start: 0.9090 (mt) cc_final: 0.8845 (mm) REVERT: C 15 MET cc_start: 0.9361 (mtm) cc_final: 0.8635 (mtt) REVERT: C 80 ASP cc_start: 0.8712 (t0) cc_final: 0.8389 (t0) REVERT: C 302 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9053 (mtp) REVERT: C 405 GLU cc_start: 0.8752 (tt0) cc_final: 0.7828 (mm-30) REVERT: D 100 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: D 305 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: D 320 MET cc_start: 0.7777 (mpp) cc_final: 0.6462 (pp-130) REVERT: D 395 ASN cc_start: 0.8925 (m-40) cc_final: 0.8491 (p0) REVERT: D 524 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8671 (tm-30) outliers start: 14 outliers final: 6 residues processed: 125 average time/residue: 1.7198 time to fit residues: 245.7173 Evaluate side-chains 113 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 524 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050776 restraints weight = 46678.314| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.20 r_work: 0.2679 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16276 Z= 0.120 Angle : 0.622 12.266 22048 Z= 0.310 Chirality : 0.043 0.237 2464 Planarity : 0.004 0.043 2844 Dihedral : 4.284 19.660 2208 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.11 % Allowed : 18.56 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2000 helix: 0.79 (0.17), residues: 968 sheet: -0.47 (0.43), residues: 168 loop : -0.88 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 319 HIS 0.005 0.001 HIS D 298 PHE 0.019 0.001 PHE B 445 TYR 0.014 0.001 TYR D 164 ARG 0.005 0.000 ARG C 414 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 690) hydrogen bonds : angle 4.83628 ( 2010) covalent geometry : bond 0.00282 (16276) covalent geometry : angle 0.62175 (22048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 3.543 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.9429 (mtm) cc_final: 0.9108 (mtm) REVERT: A 305 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9021 (mm-30) REVERT: A 320 MET cc_start: 0.7672 (mpp) cc_final: 0.6342 (pp-130) REVERT: A 416 ILE cc_start: 0.9173 (mt) cc_final: 0.8908 (mm) REVERT: B 80 ASP cc_start: 0.8948 (t0) cc_final: 0.8699 (t0) REVERT: B 294 MET cc_start: 0.8782 (mmm) cc_final: 0.8509 (mmm) REVERT: B 302 MET cc_start: 0.9431 (mtp) cc_final: 0.9146 (mtp) REVERT: B 416 ILE cc_start: 0.9117 (mt) cc_final: 0.8870 (mm) REVERT: C 15 MET cc_start: 0.9340 (mtm) cc_final: 0.8570 (mtt) REVERT: C 80 ASP cc_start: 0.8622 (t0) cc_final: 0.8370 (t0) REVERT: C 405 GLU cc_start: 0.8718 (tt0) cc_final: 0.7757 (mm-30) REVERT: D 100 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: D 305 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8773 (mm-30) REVERT: D 320 MET cc_start: 0.7659 (mpp) cc_final: 0.6379 (pp-130) REVERT: D 395 ASN cc_start: 0.8885 (m-40) cc_final: 0.8503 (p0) REVERT: D 524 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8676 (tm-30) outliers start: 19 outliers final: 6 residues processed: 122 average time/residue: 1.5885 time to fit residues: 218.9141 Evaluate side-chains 110 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 141 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051049 restraints weight = 46949.822| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.25 r_work: 0.2691 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16276 Z= 0.116 Angle : 0.622 12.279 22048 Z= 0.310 Chirality : 0.042 0.224 2464 Planarity : 0.004 0.043 2844 Dihedral : 4.231 20.139 2208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.64 % Allowed : 19.20 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 2000 helix: 0.82 (0.17), residues: 968 sheet: -0.41 (0.43), residues: 168 loop : -0.84 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 319 HIS 0.006 0.001 HIS C 28 PHE 0.020 0.001 PHE B 445 TYR 0.014 0.001 TYR B 208 ARG 0.010 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 690) hydrogen bonds : angle 4.81007 ( 2010) covalent geometry : bond 0.00271 (16276) covalent geometry : angle 0.62231 (22048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9435 (mtm) cc_final: 0.9132 (mtm) REVERT: A 80 ASP cc_start: 0.9140 (t0) cc_final: 0.8579 (t0) REVERT: A 305 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9024 (mm-30) REVERT: A 320 MET cc_start: 0.7451 (mpp) cc_final: 0.6093 (pp-130) REVERT: A 416 ILE cc_start: 0.9175 (mt) cc_final: 0.8925 (mm) REVERT: B 15 MET cc_start: 0.9323 (mtt) cc_final: 0.8867 (mtt) REVERT: B 294 MET cc_start: 0.8775 (mmm) cc_final: 0.8505 (mmm) REVERT: B 302 MET cc_start: 0.9414 (mtp) cc_final: 0.9142 (mtp) REVERT: B 416 ILE cc_start: 0.9113 (mt) cc_final: 0.8881 (mm) REVERT: B 551 MET cc_start: 0.8750 (ptm) cc_final: 0.8186 (ptp) REVERT: C 15 MET cc_start: 0.9306 (mtm) cc_final: 0.8403 (mtp) REVERT: C 80 ASP cc_start: 0.8664 (t0) cc_final: 0.8389 (t0) REVERT: C 405 GLU cc_start: 0.8762 (tt0) cc_final: 0.7811 (mm-30) REVERT: D 305 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8814 (mm-30) REVERT: D 320 MET cc_start: 0.7641 (mpp) cc_final: 0.6317 (pp-130) REVERT: D 395 ASN cc_start: 0.8879 (m-40) cc_final: 0.8486 (p0) REVERT: D 524 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8679 (tm-30) outliers start: 11 outliers final: 6 residues processed: 117 average time/residue: 1.1089 time to fit residues: 147.1828 Evaluate side-chains 110 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047553 restraints weight = 47183.559| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.22 r_work: 0.2590 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16276 Z= 0.260 Angle : 0.687 12.869 22048 Z= 0.345 Chirality : 0.045 0.219 2464 Planarity : 0.005 0.076 2844 Dihedral : 4.373 22.595 2208 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.70 % Allowed : 19.38 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 2000 helix: 0.96 (0.17), residues: 964 sheet: -0.43 (0.43), residues: 168 loop : -0.76 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 546 HIS 0.009 0.001 HIS C 28 PHE 0.023 0.002 PHE D 84 TYR 0.017 0.002 TYR C 74 ARG 0.018 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 690) hydrogen bonds : angle 4.97834 ( 2010) covalent geometry : bond 0.00599 (16276) covalent geometry : angle 0.68677 (22048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10456.29 seconds wall clock time: 186 minutes 49.60 seconds (11209.60 seconds total)