Starting phenix.real_space_refine on Tue Dec 31 12:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e76_27936/12_2024/8e76_27936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e76_27936/12_2024/8e76_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_27936/12_2024/8e76_27936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e76_27936/12_2024/8e76_27936.map" model { file = "/net/cci-nas-00/data/ceres_data/8e76_27936/12_2024/8e76_27936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e76_27936/12_2024/8e76_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-5532/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: 8.12, per 1000 atoms: 0.51 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: 3.60 Conformation dependent library (CDL) restraints added in 2.0 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: 1.93 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: 5.60 Time building geometry restraints manager: 4.20 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: 0.00 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: 0.890 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.400 ------------------------------------------------------------------------------- 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= 0.483 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 *********************** 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 : 1.770 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: 1.0736 time to fit residues: 400.1095 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 : 1.799 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 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= 0.275 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 *********************** 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 : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.5426 (mmm) cc_final: 0.5183 (mmm) REVERT: B 406 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5504 (mttt) REVERT: C 63 MET cc_start: 0.6306 (mmp) cc_final: 0.5958 (mmp) REVERT: D 304 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7344 (mm) outliers start: 36 outliers final: 9 residues processed: 216 average time/residue: 0.8918 time to fit residues: 224.1361 Evaluate side-chains 173 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN B 28 HIS C 119 HIS ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 16276 Z= 0.290 Angle : 0.653 10.590 22048 Z= 0.336 Chirality : 0.045 0.209 2464 Planarity : 0.005 0.092 2844 Dihedral : 4.714 20.636 2208 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.75 % Allowed : 14.11 % Favored : 83.14 % 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: -0.74 (0.19), residues: 2000 helix: 0.31 (0.17), residues: 960 sheet: -0.28 (0.42), residues: 168 loop : -1.41 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 319 HIS 0.007 0.001 HIS B 298 PHE 0.020 0.002 PHE D 526 TYR 0.026 0.002 TYR D 164 ARG 0.037 0.001 ARG C 485 *********************** 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 206 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 395 ASN cc_start: 0.7543 (p0) cc_final: 0.7263 (p0) REVERT: B 406 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5645 (mttt) REVERT: D 100 TYR cc_start: 0.5314 (OUTLIER) cc_final: 0.5050 (m-80) outliers start: 47 outliers final: 4 residues processed: 194 average time/residue: 0.8884 time to fit residues: 201.0186 Evaluate side-chains 143 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 406 LYS Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 551 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 ASN C 230 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16276 Z= 0.341 Angle : 0.688 10.423 22048 Z= 0.357 Chirality : 0.046 0.227 2464 Planarity : 0.005 0.084 2844 Dihedral : 4.675 22.490 2208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.52 % Allowed : 14.87 % Favored : 82.61 % 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: -0.51 (0.19), residues: 2000 helix: 0.45 (0.17), residues: 960 sheet: -0.54 (0.43), residues: 164 loop : -1.13 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 319 HIS 0.017 0.001 HIS C 480 PHE 0.026 0.002 PHE A 104 TYR 0.015 0.002 TYR A 49 ARG 0.006 0.001 ARG A 106 *********************** 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 182 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: D 100 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.5063 (m-80) outliers start: 43 outliers final: 4 residues processed: 172 average time/residue: 1.0262 time to fit residues: 202.6094 Evaluate side-chains 118 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 100 TYR 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 161 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 143 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16276 Z= 0.192 Angle : 0.600 10.780 22048 Z= 0.305 Chirality : 0.043 0.235 2464 Planarity : 0.004 0.049 2844 Dihedral : 4.493 20.492 2208 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.11 % Allowed : 17.04 % Favored : 81.85 % 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: -0.34 (0.19), residues: 2000 helix: 0.60 (0.17), residues: 968 sheet: -0.38 (0.42), residues: 168 loop : -1.09 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 319 HIS 0.007 0.001 HIS B 298 PHE 0.019 0.002 PHE A 445 TYR 0.015 0.001 TYR D 487 ARG 0.010 0.000 ARG C 485 *********************** 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 148 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 1.1068 time to fit residues: 183.2267 Evaluate side-chains 115 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 397 THR 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 65 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 101 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16276 Z= 0.173 Angle : 0.613 20.620 22048 Z= 0.307 Chirality : 0.043 0.242 2464 Planarity : 0.004 0.045 2844 Dihedral : 4.316 20.614 2208 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.29 % Allowed : 17.15 % Favored : 81.56 % 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: -0.23 (0.19), residues: 2000 helix: 0.69 (0.17), residues: 968 sheet: -0.35 (0.43), residues: 168 loop : -1.03 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 319 HIS 0.006 0.001 HIS A 28 PHE 0.019 0.002 PHE A 445 TYR 0.013 0.001 TYR D 487 ARG 0.009 0.000 ARG A 108 *********************** 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 140 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: B 63 MET cc_start: 0.6490 (mmp) cc_final: 0.6049 (mmp) outliers start: 22 outliers final: 8 residues processed: 136 average time/residue: 1.0217 time to fit residues: 160.4435 Evaluate side-chains 119 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 397 THR 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 186 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16276 Z= 0.267 Angle : 0.625 13.860 22048 Z= 0.312 Chirality : 0.044 0.289 2464 Planarity : 0.004 0.048 2844 Dihedral : 4.282 20.256 2208 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.00 % Allowed : 17.68 % Favored : 81.32 % 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: -0.11 (0.19), residues: 2000 helix: 0.76 (0.17), residues: 972 sheet: -0.34 (0.43), residues: 168 loop : -0.92 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 319 HIS 0.008 0.001 HIS C 480 PHE 0.020 0.002 PHE C 104 TYR 0.013 0.001 TYR D 487 ARG 0.011 0.000 ARG C 387 *********************** 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 131 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7207 (mtt) cc_final: 0.6973 (mtm) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 1.0653 time to fit residues: 155.0891 Evaluate side-chains 111 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 364 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 397 THR 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 119 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16276 Z= 0.219 Angle : 0.621 15.404 22048 Z= 0.309 Chirality : 0.044 0.300 2464 Planarity : 0.004 0.049 2844 Dihedral : 4.258 19.588 2208 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.05 % Allowed : 17.97 % Favored : 80.97 % 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: -0.11 (0.19), residues: 2000 helix: 0.77 (0.17), residues: 968 sheet: -0.37 (0.43), residues: 168 loop : -0.92 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 319 HIS 0.005 0.001 HIS A 28 PHE 0.019 0.002 PHE A 445 TYR 0.015 0.001 TYR D 487 ARG 0.012 0.000 ARG D 106 *********************** 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 129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6901 (mtt) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 1.1612 time to fit residues: 164.5633 Evaluate side-chains 111 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16276 Z= 0.222 Angle : 0.639 16.469 22048 Z= 0.316 Chirality : 0.044 0.304 2464 Planarity : 0.004 0.056 2844 Dihedral : 4.250 19.559 2208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.88 % Allowed : 18.56 % 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: -0.06 (0.19), residues: 2000 helix: 0.81 (0.17), residues: 968 sheet: -0.37 (0.43), residues: 168 loop : -0.90 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 319 HIS 0.006 0.001 HIS A 28 PHE 0.044 0.002 PHE B 434 TYR 0.016 0.001 TYR B 408 ARG 0.011 0.000 ARG D 106 *********************** 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 121 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: C 15 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6704 (mtt) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 1.0965 time to fit residues: 145.1634 Evaluate side-chains 107 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 163 LEU 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 115 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16276 Z= 0.285 Angle : 0.670 19.013 22048 Z= 0.332 Chirality : 0.044 0.282 2464 Planarity : 0.004 0.051 2844 Dihedral : 4.309 24.693 2208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.59 % Allowed : 19.15 % Favored : 80.27 % 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: 0.80 (0.17), residues: 976 sheet: -0.40 (0.43), residues: 168 loop : -0.92 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 546 HIS 0.007 0.001 HIS D 298 PHE 0.041 0.002 PHE B 434 TYR 0.013 0.001 TYR C 164 ARG 0.011 0.000 ARG D 106 ********************** 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 107 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: C 15 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6730 (mtm) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 1.1490 time to fit residues: 139.4892 Evaluate side-chains 101 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain D residue 163 LEU 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 48 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.069176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051276 restraints weight = 46256.079| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.26 r_work: 0.2692 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16276 Z= 0.184 Angle : 0.658 19.460 22048 Z= 0.324 Chirality : 0.043 0.286 2464 Planarity : 0.004 0.042 2844 Dihedral : 4.261 23.535 2208 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.59 % Allowed : 19.38 % Favored : 80.04 % 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: 0.79 (0.17), residues: 972 sheet: -0.35 (0.43), residues: 168 loop : -0.98 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 546 HIS 0.006 0.001 HIS D 298 PHE 0.035 0.002 PHE B 434 TYR 0.013 0.001 TYR C 164 ARG 0.009 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4105.86 seconds wall clock time: 76 minutes 2.34 seconds (4562.34 seconds total)