Starting phenix.real_space_refine on Tue Nov 19 01:56:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/11_2024/8f0a_28754.cif" } resolution = 2.6 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= 0.001 sd= 0.053 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 5547 2.51 5 N 1566 2.21 5 O 1716 1.98 5 H 9189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18060 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "E" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "a" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: D, F, C, B, c, b Time building chain proxies: 10.90, per 1000 atoms: 0.60 Number of scatterers: 18060 At special positions: 0 Unit cell: (98.58, 112.36, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 1716 8.00 N 1566 7.00 C 5547 6.00 H 9189 1.00 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: 4.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 23.3% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.610A pdb=" N GLN A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 24 Proline residue: B 24 - end of helix No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 21 through 24 Proline residue: C 24 - end of helix No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 320 through 329 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'a' and resid 37 through 49 Processing helix chain 'b' and resid 37 through 49 Processing helix chain 'c' and resid 37 through 49 Processing sheet with id=AA1, first strand: chain 'a' and resid 34 through 36 removed outlier: 4.250A pdb=" N MET A 85 " --> pdb=" O PHE a 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A 89 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A 103 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 99 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 136 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 130 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 138 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET A 127 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR A 111 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 32 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 113 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 30 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 115 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 28 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN A 225 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 242 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 200 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A 185 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 214 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY A 340 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 338 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 34 through 36 removed outlier: 4.253A pdb=" N MET B 85 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 89 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 103 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 99 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 136 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 130 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 138 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 113 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET B 127 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR B 111 " --> pdb=" O MET B 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 32 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 113 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 30 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 115 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 28 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 29 through 31 removed outlier: 5.793A pdb=" N ASN B 225 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 242 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN B 200 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU B 185 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 214 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AA9, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY B 340 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 313 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 338 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.662A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET C 85 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 89 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C 103 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 99 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 136 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS C 130 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 138 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 113 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET C 127 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR C 111 " --> pdb=" O MET C 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU C 32 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 113 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 30 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 115 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 28 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN C 225 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 242 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN C 200 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU C 185 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 214 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.566A pdb=" N GLY C 340 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 313 " --> pdb=" O THR C 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 338 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.663A pdb=" N MET C 268 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN D 435 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 410 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 433 " --> pdb=" O ALA D 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN E 435 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 410 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA E 433 " --> pdb=" O ALA E 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN F 435 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 410 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA F 433 " --> pdb=" O ALA F 410 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1062 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: 13.76 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 9189 1.13 - 1.30: 1766 1.30 - 1.48: 3762 1.48 - 1.65: 3340 1.65 - 1.83: 84 Bond restraints: 18141 Sorted by residual: bond pdb=" CB HIS a 33 " pdb=" CG HIS a 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS b 33 " pdb=" CG HIS b 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB HIS c 33 " pdb=" CG HIS c 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB LEU b 32 " pdb=" CG LEU b 32 " ideal model delta sigma weight residual 1.530 1.327 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CB LEU c 32 " pdb=" CG LEU c 32 " ideal model delta sigma weight residual 1.530 1.328 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 18136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27507 2.41 - 4.83: 3614 4.83 - 7.24: 1568 7.24 - 9.66: 266 9.66 - 12.07: 9 Bond angle restraints: 32964 Sorted by residual: angle pdb=" C ASP A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" C ASP B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 119.56 127.65 -8.09 1.02e+00 9.61e-01 6.29e+01 angle pdb=" N LEU b 32 " pdb=" CA LEU b 32 " pdb=" C LEU b 32 " ideal model delta sigma weight residual 110.68 121.67 -10.99 1.39e+00 5.18e-01 6.25e+01 angle pdb=" N LEU a 32 " pdb=" CA LEU a 32 " pdb=" C LEU a 32 " ideal model delta sigma weight residual 110.68 121.66 -10.98 1.39e+00 5.18e-01 6.24e+01 angle pdb=" C ASP C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.22e+01 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 7933 16.51 - 33.03: 273 33.03 - 49.54: 116 49.54 - 66.05: 42 66.05 - 82.57: 9 Dihedral angle restraints: 8373 sinusoidal: 4749 harmonic: 3624 Sorted by residual: dihedral pdb=" CD2 HIS B 105 " pdb=" CG HIS B 105 " pdb=" ND1 HIS B 105 " pdb=" HD1 HIS B 105 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS C 105 " pdb=" CG HIS C 105 " pdb=" ND1 HIS C 105 " pdb=" HD1 HIS C 105 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS A 105 " pdb=" CG HIS A 105 " pdb=" ND1 HIS A 105 " pdb=" HD1 HIS A 105 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 858 0.110 - 0.219: 457 0.219 - 0.328: 111 0.328 - 0.438: 14 0.438 - 0.547: 9 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CG LEU C 87 " pdb=" CB LEU C 87 " pdb=" CD1 LEU C 87 " pdb=" CD2 LEU C 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" CG LEU A 87 " pdb=" CB LEU A 87 " pdb=" CD1 LEU A 87 " pdb=" CD2 LEU A 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 1446 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 105 " 0.076 2.00e-02 2.50e+03 7.53e-02 1.28e+02 pdb=" CG HIS B 105 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS B 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS B 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS B 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS B 105 " -0.173 2.00e-02 2.50e+03 pdb=" HD2 HIS B 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS B 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 105 " -0.076 2.00e-02 2.50e+03 7.52e-02 1.27e+02 pdb=" CG HIS C 105 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS C 105 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS C 105 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS C 105 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 105 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS C 105 " 0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS C 105 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS C 105 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.26e+02 pdb=" CG HIS A 105 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS A 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS A 105 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS A 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS A 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS A 105 " 0.057 2.00e-02 2.50e+03 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 418 2.00 - 2.65: 24724 2.65 - 3.30: 52799 3.30 - 3.95: 71192 3.95 - 4.60: 110521 Nonbonded interactions: 259654 Sorted by model distance: nonbonded pdb=" H SER B 134 " pdb=" H ASP B 135 " model vdw 1.353 2.100 nonbonded pdb=" H SER A 134 " pdb=" H ASP A 135 " model vdw 1.355 2.100 nonbonded pdb=" H SER C 134 " pdb=" H ASP C 135 " model vdw 1.355 2.100 nonbonded pdb=" HZ3 LYS B 114 " pdb=" OD1 ASP B 124 " model vdw 1.618 2.450 nonbonded pdb=" HZ3 LYS A 114 " pdb=" OD1 ASP A 124 " model vdw 1.618 2.450 ... (remaining 259649 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 51.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 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:15.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 : 0.031 0.203 8952 Z= 2.053 Angle : 1.768 10.986 12084 Z= 1.183 Chirality : 0.132 0.547 1449 Planarity : 0.010 0.075 1578 Dihedral : 9.862 82.565 3327 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1188 helix: -0.93 (0.30), residues: 231 sheet: 1.04 (0.28), residues: 366 loop : 0.92 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP a 48 HIS 0.005 0.002 HIS A 105 PHE 0.018 0.007 PHE B 198 TYR 0.058 0.009 TYR B 257 ARG 0.015 0.002 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.7805 (t0) cc_final: 0.7268 (t0) REVERT: A 193 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8716 (tp30) REVERT: B 191 ASN cc_start: 0.7695 (t0) cc_final: 0.7102 (t0) REVERT: B 193 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8711 (tp30) REVERT: C 191 ASN cc_start: 0.7626 (t0) cc_final: 0.6961 (t0) REVERT: C 193 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8728 (tp30) REVERT: D 378 ASN cc_start: 0.8296 (m-40) cc_final: 0.8072 (t0) REVERT: D 389 ASN cc_start: 0.9496 (t0) cc_final: 0.8521 (t0) REVERT: D 437 GLN cc_start: 0.7803 (mt0) cc_final: 0.7371 (tp-100) REVERT: E 378 ASN cc_start: 0.8307 (m-40) cc_final: 0.7973 (t0) REVERT: E 389 ASN cc_start: 0.9507 (t0) cc_final: 0.8702 (t0) REVERT: E 415 VAL cc_start: 0.8418 (t) cc_final: 0.8076 (p) REVERT: F 378 ASN cc_start: 0.8161 (m-40) cc_final: 0.7921 (t0) REVERT: F 389 ASN cc_start: 0.9440 (t0) cc_final: 0.8742 (t0) REVERT: F 415 VAL cc_start: 0.8678 (t) cc_final: 0.8345 (p) REVERT: F 424 VAL cc_start: 0.9198 (t) cc_final: 0.8960 (m) REVERT: F 437 GLN cc_start: 0.8004 (mt0) cc_final: 0.7599 (tp-100) outliers start: 0 outliers final: 2 residues processed: 255 average time/residue: 3.0531 time to fit residues: 825.3878 Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 440 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.6770 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.247 Angle : 0.692 6.262 12084 Z= 0.386 Chirality : 0.049 0.184 1449 Planarity : 0.004 0.045 1578 Dihedral : 7.311 86.253 1264 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.02 % Allowed : 11.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1188 helix: 1.10 (0.36), residues: 228 sheet: 0.63 (0.26), residues: 384 loop : 0.75 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP a 48 HIS 0.007 0.003 HIS c 33 PHE 0.012 0.002 PHE B 198 TYR 0.009 0.001 TYR b 34 ARG 0.007 0.001 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8967 (mp0) REVERT: B 191 ASN cc_start: 0.7472 (t0) cc_final: 0.6976 (t0) REVERT: B 193 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8764 (tp30) REVERT: C 12 MET cc_start: 0.6701 (mtp) cc_final: 0.6465 (mtp) REVERT: C 85 MET cc_start: 0.8753 (mtm) cc_final: 0.8509 (mtp) REVERT: C 191 ASN cc_start: 0.7438 (t0) cc_final: 0.7017 (t0) REVERT: C 193 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8770 (tp30) REVERT: D 378 ASN cc_start: 0.8418 (m-40) cc_final: 0.8196 (t0) REVERT: D 389 ASN cc_start: 0.9031 (t0) cc_final: 0.8736 (t0) REVERT: D 415 VAL cc_start: 0.8694 (t) cc_final: 0.8354 (p) REVERT: D 437 GLN cc_start: 0.7877 (mt0) cc_final: 0.7588 (tp-100) REVERT: E 378 ASN cc_start: 0.8615 (m-40) cc_final: 0.8268 (t0) REVERT: E 389 ASN cc_start: 0.9308 (t0) cc_final: 0.8930 (t0) REVERT: E 415 VAL cc_start: 0.8500 (t) cc_final: 0.8259 (p) REVERT: E 437 GLN cc_start: 0.8156 (mt0) cc_final: 0.7937 (tp-100) REVERT: E 438 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7449 (mtt90) REVERT: F 375 GLU cc_start: 0.9317 (mp0) cc_final: 0.9101 (mp0) REVERT: F 378 ASN cc_start: 0.8514 (m-40) cc_final: 0.8205 (t0) REVERT: F 389 ASN cc_start: 0.9264 (t0) cc_final: 0.8933 (t0) REVERT: F 415 VAL cc_start: 0.8538 (t) cc_final: 0.8257 (p) REVERT: F 426 ASP cc_start: 0.9778 (m-30) cc_final: 0.9562 (p0) outliers start: 19 outliers final: 6 residues processed: 239 average time/residue: 2.8472 time to fit residues: 723.8591 Evaluate side-chains 224 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain c residue 38 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8952 Z= 0.360 Angle : 0.619 6.331 12084 Z= 0.338 Chirality : 0.047 0.157 1449 Planarity : 0.005 0.071 1578 Dihedral : 7.069 85.296 1260 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.80 % Allowed : 12.53 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1188 helix: 1.70 (0.38), residues: 228 sheet: 0.39 (0.27), residues: 354 loop : 0.55 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 48 HIS 0.006 0.003 HIS c 33 PHE 0.010 0.001 PHE B 123 TYR 0.007 0.001 TYR b 34 ARG 0.009 0.001 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: A 193 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8642 (tm-30) REVERT: A 271 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 133 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7976 (mmm-85) REVERT: B 193 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8686 (tp30) REVERT: B 271 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: C 12 MET cc_start: 0.6623 (mtp) cc_final: 0.6381 (mtp) REVERT: C 191 ASN cc_start: 0.7587 (t0) cc_final: 0.7211 (t0) REVERT: C 193 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8787 (tp30) REVERT: D 378 ASN cc_start: 0.8466 (m-40) cc_final: 0.8251 (t0) REVERT: D 389 ASN cc_start: 0.9060 (t0) cc_final: 0.8789 (t0) REVERT: D 437 GLN cc_start: 0.7905 (mt0) cc_final: 0.7439 (tm130) REVERT: E 378 ASN cc_start: 0.8624 (m-40) cc_final: 0.8261 (t0) REVERT: E 389 ASN cc_start: 0.9314 (t0) cc_final: 0.9050 (t0) REVERT: E 413 GLN cc_start: 0.9292 (mm-40) cc_final: 0.9037 (mm-40) REVERT: E 437 GLN cc_start: 0.8055 (mt0) cc_final: 0.7697 (tm130) REVERT: E 438 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7619 (mtt180) REVERT: F 378 ASN cc_start: 0.8535 (m-40) cc_final: 0.8237 (t0) REVERT: F 389 ASN cc_start: 0.9253 (t0) cc_final: 0.9030 (t0) REVERT: F 415 VAL cc_start: 0.8691 (t) cc_final: 0.8484 (p) outliers start: 17 outliers final: 9 residues processed: 217 average time/residue: 2.9802 time to fit residues: 686.7225 Evaluate side-chains 219 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8952 Z= 0.213 Angle : 0.591 8.198 12084 Z= 0.313 Chirality : 0.046 0.155 1449 Planarity : 0.004 0.049 1578 Dihedral : 7.074 84.906 1260 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.49 % Allowed : 14.54 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1188 helix: 1.80 (0.38), residues: 228 sheet: 0.50 (0.27), residues: 339 loop : 0.40 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP a 48 HIS 0.004 0.002 HIS a 33 PHE 0.008 0.001 PHE C 123 TYR 0.004 0.001 TYR b 34 ARG 0.006 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7760 (mmt90) REVERT: A 193 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8698 (tm-30) REVERT: B 193 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8715 (tp30) REVERT: C 12 MET cc_start: 0.6535 (mtp) cc_final: 0.6265 (mtt) REVERT: C 191 ASN cc_start: 0.7586 (t0) cc_final: 0.7124 (t0) REVERT: C 193 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8814 (tp30) REVERT: D 378 ASN cc_start: 0.8487 (m-40) cc_final: 0.8284 (t0) REVERT: D 426 ASP cc_start: 0.9761 (m-30) cc_final: 0.9548 (p0) REVERT: D 437 GLN cc_start: 0.8060 (mt0) cc_final: 0.7822 (tm130) REVERT: E 378 ASN cc_start: 0.8670 (m-40) cc_final: 0.8322 (t0) REVERT: E 413 GLN cc_start: 0.9314 (mm-40) cc_final: 0.9057 (mm110) REVERT: E 437 GLN cc_start: 0.8100 (mt0) cc_final: 0.7658 (tm130) REVERT: E 438 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7530 (mtt180) REVERT: F 378 ASN cc_start: 0.8577 (m-40) cc_final: 0.8285 (t0) REVERT: F 415 VAL cc_start: 0.8693 (t) cc_final: 0.8486 (p) outliers start: 14 outliers final: 8 residues processed: 220 average time/residue: 2.9575 time to fit residues: 692.6283 Evaluate side-chains 217 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 440 ASP Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.223 Angle : 0.581 7.392 12084 Z= 0.306 Chirality : 0.046 0.151 1449 Planarity : 0.004 0.052 1578 Dihedral : 7.001 84.594 1260 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.96 % Allowed : 15.92 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1188 helix: 1.81 (0.38), residues: 228 sheet: 0.31 (0.27), residues: 354 loop : 0.53 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.004 0.002 HIS c 33 PHE 0.010 0.001 PHE b 36 TYR 0.004 0.001 TYR b 34 ARG 0.010 0.001 ARG D 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7783 (mmt90) REVERT: A 193 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8685 (tm-30) REVERT: A 271 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8201 (mm-30) REVERT: B 133 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: B 193 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8624 (tp30) REVERT: C 191 ASN cc_start: 0.7518 (t0) cc_final: 0.7058 (t0) REVERT: C 193 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8810 (tp30) REVERT: D 376 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6623 (pmm) REVERT: D 378 ASN cc_start: 0.8619 (m-40) cc_final: 0.8395 (t0) REVERT: D 426 ASP cc_start: 0.9765 (m-30) cc_final: 0.9542 (p0) REVERT: D 437 GLN cc_start: 0.8042 (mt0) cc_final: 0.7796 (tm130) REVERT: E 378 ASN cc_start: 0.8624 (m-40) cc_final: 0.8277 (t0) REVERT: E 413 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9105 (mm-40) REVERT: E 437 GLN cc_start: 0.8086 (mt0) cc_final: 0.7660 (tm130) REVERT: E 438 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7600 (mtt180) REVERT: F 378 ASN cc_start: 0.8608 (m-40) cc_final: 0.8305 (t0) outliers start: 9 outliers final: 4 residues processed: 214 average time/residue: 2.9546 time to fit residues: 671.9253 Evaluate side-chains 216 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8952 Z= 0.265 Angle : 0.590 8.466 12084 Z= 0.311 Chirality : 0.046 0.148 1449 Planarity : 0.004 0.058 1578 Dihedral : 6.949 84.151 1260 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.70 % Allowed : 15.50 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1188 helix: 1.70 (0.37), residues: 231 sheet: 0.42 (0.27), residues: 339 loop : 0.41 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP c 48 HIS 0.004 0.002 HIS c 33 PHE 0.010 0.001 PHE b 36 TYR 0.005 0.001 TYR F 444 ARG 0.007 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8042 (mmm-85) REVERT: A 193 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8825 (tp30) REVERT: A 271 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8189 (mm-30) REVERT: B 133 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7874 (mmm-85) REVERT: B 193 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8616 (tp30) REVERT: C 191 ASN cc_start: 0.7505 (t0) cc_final: 0.7052 (t0) REVERT: C 193 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8804 (tp30) REVERT: D 376 MET cc_start: 0.7093 (pmt) cc_final: 0.6615 (pmm) REVERT: D 378 ASN cc_start: 0.8643 (m-40) cc_final: 0.8381 (t0) REVERT: D 426 ASP cc_start: 0.9760 (m-30) cc_final: 0.9539 (p0) REVERT: D 437 GLN cc_start: 0.8021 (mt0) cc_final: 0.7739 (tm130) REVERT: E 376 MET cc_start: 0.6698 (pmt) cc_final: 0.6211 (pmm) REVERT: E 378 ASN cc_start: 0.8689 (m-40) cc_final: 0.8359 (t0) REVERT: E 413 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9110 (mm-40) REVERT: E 437 GLN cc_start: 0.8129 (mt0) cc_final: 0.7684 (tm130) REVERT: E 438 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7735 (mtt90) REVERT: F 378 ASN cc_start: 0.8642 (m-40) cc_final: 0.8334 (t0) outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 3.0307 time to fit residues: 676.3515 Evaluate side-chains 216 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain F residue 440 ASP Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8952 Z= 0.221 Angle : 0.585 8.954 12084 Z= 0.305 Chirality : 0.046 0.157 1449 Planarity : 0.004 0.058 1578 Dihedral : 6.943 83.565 1260 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.96 % Allowed : 17.20 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1188 helix: 1.80 (0.37), residues: 231 sheet: 0.44 (0.27), residues: 339 loop : 0.48 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP c 48 HIS 0.004 0.002 HIS b 33 PHE 0.010 0.001 PHE b 36 TYR 0.004 0.001 TYR b 34 ARG 0.007 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: A 193 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8832 (tp30) REVERT: A 271 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8164 (mm-30) REVERT: B 133 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: B 193 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8593 (tp30) REVERT: B 286 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7733 (mtt-85) REVERT: C 191 ASN cc_start: 0.7473 (t0) cc_final: 0.7019 (t0) REVERT: C 193 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8775 (tp30) REVERT: D 376 MET cc_start: 0.7010 (pmt) cc_final: 0.6556 (pmm) REVERT: D 378 ASN cc_start: 0.8652 (m-40) cc_final: 0.8391 (t0) REVERT: D 426 ASP cc_start: 0.9768 (m-30) cc_final: 0.9549 (p0) REVERT: D 437 GLN cc_start: 0.8021 (mt0) cc_final: 0.7767 (tm130) REVERT: E 376 MET cc_start: 0.6693 (pmt) cc_final: 0.6145 (pmm) REVERT: E 378 ASN cc_start: 0.8698 (m-40) cc_final: 0.8392 (t0) REVERT: E 413 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9122 (mm-40) REVERT: E 417 ASN cc_start: 0.8376 (p0) cc_final: 0.8167 (p0) REVERT: E 437 GLN cc_start: 0.8084 (mt0) cc_final: 0.7637 (tm130) REVERT: E 438 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7796 (mtt90) REVERT: F 378 ASN cc_start: 0.8641 (m-40) cc_final: 0.8353 (t0) outliers start: 9 outliers final: 5 residues processed: 214 average time/residue: 2.9408 time to fit residues: 668.5479 Evaluate side-chains 213 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8952 Z= 0.271 Angle : 0.617 10.414 12084 Z= 0.320 Chirality : 0.046 0.170 1449 Planarity : 0.004 0.061 1578 Dihedral : 6.923 82.781 1260 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.06 % Allowed : 18.15 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.24), residues: 1188 helix: 1.87 (0.37), residues: 231 sheet: 0.25 (0.26), residues: 354 loop : 0.59 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 48 HIS 0.004 0.002 HIS b 33 PHE 0.023 0.001 PHE a 36 TYR 0.005 0.001 TYR b 34 ARG 0.007 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8072 (mmm-85) REVERT: A 193 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8833 (tp30) REVERT: A 271 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: B 133 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: B 193 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8603 (tp30) REVERT: C 191 ASN cc_start: 0.7460 (t0) cc_final: 0.7032 (t0) REVERT: C 193 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8779 (tp30) REVERT: D 376 MET cc_start: 0.7091 (pmt) cc_final: 0.6637 (pmm) REVERT: D 378 ASN cc_start: 0.8688 (m-40) cc_final: 0.8443 (t0) REVERT: D 426 ASP cc_start: 0.9763 (m-30) cc_final: 0.9550 (p0) REVERT: D 437 GLN cc_start: 0.8004 (mt0) cc_final: 0.7708 (tm130) REVERT: E 376 MET cc_start: 0.6522 (pmt) cc_final: 0.6020 (pmm) REVERT: E 378 ASN cc_start: 0.8712 (m-40) cc_final: 0.8399 (t0) REVERT: E 413 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9106 (mm-40) REVERT: E 417 ASN cc_start: 0.8403 (p0) cc_final: 0.8193 (p0) REVERT: E 437 GLN cc_start: 0.8104 (mt0) cc_final: 0.7650 (tm130) REVERT: F 376 MET cc_start: 0.7662 (pmm) cc_final: 0.7326 (pmm) REVERT: F 378 ASN cc_start: 0.8676 (m-40) cc_final: 0.8370 (t0) outliers start: 10 outliers final: 5 residues processed: 208 average time/residue: 2.9542 time to fit residues: 653.5615 Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 205 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 426 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4529 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: