Starting phenix.real_space_refine on Fri Sep 27 14:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/09_2024/6z7q_11112.cif" } resolution = 3.8 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= 0.003 sd= 0.975 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 60 5.16 5 C 10575 2.51 5 N 2880 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16665 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.31, per 1000 atoms: 0.44 Number of scatterers: 16665 At special positions: 0 Unit cell: (121.797, 122.838, 111.387, 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 60 16.00 O 3150 8.00 N 2880 7.00 C 10575 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: 3.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3950 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 35 sheets defined 7.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 190 removed outlier: 3.504A pdb=" N ILE C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 190 removed outlier: 3.504A pdb=" N ILE D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR D 188 " --> pdb=" O ILE D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 296 removed outlier: 3.501A pdb=" N GLU E 289 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 292 " --> pdb=" O TYR E 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 294 " --> pdb=" O ALA E 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.654A pdb=" N PHE A 141 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 164 " --> pdb=" O PHE A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP A 322 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP A 376 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 402 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 374 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL A 453 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE B 141 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 164 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322 removed outlier: 4.354A pdb=" N ASP B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP B 376 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL B 402 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 374 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL B 453 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE C 141 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 164 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 148 Processing sheet with id=AC1, first strand: chain 'C' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP C 322 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP C 376 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL C 402 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL C 374 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.568A pdb=" N VAL C 453 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AC5, first strand: chain 'D' and resid 125 through 126 Processing sheet with id=AC6, first strand: chain 'D' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE D 141 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 164 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AC8, first strand: chain 'D' and resid 321 through 322 removed outlier: 4.356A pdb=" N ASP D 322 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP D 376 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL D 402 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL D 374 " --> pdb=" O VAL D 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 410 through 413 removed outlier: 3.568A pdb=" N VAL D 453 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AD3, first strand: chain 'E' and resid 125 through 126 Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 143 removed outlier: 3.654A pdb=" N PHE E 141 " --> pdb=" O PHE E 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 164 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AD6, first strand: chain 'E' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP E 322 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP E 376 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL E 402 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL E 374 " --> pdb=" O VAL E 402 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL E 453 " --> pdb=" O LYS E 410 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 4.63 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: 5490 1.34 - 1.46: 3821 1.46 - 1.58: 7624 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 17040 Sorted by residual: bond pdb=" C PHE E 232 " pdb=" N HIS E 233 " ideal model delta sigma weight residual 1.333 1.294 0.039 2.74e-02 1.33e+03 2.00e+00 bond pdb=" C PHE D 232 " pdb=" N HIS D 233 " ideal model delta sigma weight residual 1.333 1.294 0.039 2.74e-02 1.33e+03 1.98e+00 bond pdb=" C PHE B 232 " pdb=" N HIS B 233 " ideal model delta sigma weight residual 1.333 1.294 0.038 2.74e-02 1.33e+03 1.97e+00 bond pdb=" C PHE A 232 " pdb=" N HIS A 233 " ideal model delta sigma weight residual 1.333 1.294 0.038 2.74e-02 1.33e+03 1.96e+00 bond pdb=" C PHE C 232 " pdb=" N HIS C 233 " ideal model delta sigma weight residual 1.333 1.295 0.038 2.74e-02 1.33e+03 1.91e+00 ... (remaining 17035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 20635 1.12 - 2.25: 2030 2.25 - 3.37: 383 3.37 - 4.49: 87 4.49 - 5.62: 40 Bond angle restraints: 23175 Sorted by residual: angle pdb=" N LEU C 80 " pdb=" CA LEU C 80 " pdb=" C LEU C 80 " ideal model delta sigma weight residual 112.97 110.14 2.83 1.06e+00 8.90e-01 7.14e+00 angle pdb=" N LEU B 80 " pdb=" CA LEU B 80 " pdb=" C LEU B 80 " ideal model delta sigma weight residual 112.97 110.14 2.83 1.06e+00 8.90e-01 7.13e+00 angle pdb=" N LEU E 80 " pdb=" CA LEU E 80 " pdb=" C LEU E 80 " ideal model delta sigma weight residual 112.97 110.16 2.81 1.06e+00 8.90e-01 7.01e+00 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 112.97 110.17 2.80 1.06e+00 8.90e-01 6.98e+00 angle pdb=" N LEU D 80 " pdb=" CA LEU D 80 " pdb=" C LEU D 80 " ideal model delta sigma weight residual 112.97 110.18 2.79 1.06e+00 8.90e-01 6.93e+00 ... (remaining 23170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9116 17.00 - 34.00: 976 34.00 - 51.01: 128 51.01 - 68.01: 20 68.01 - 85.01: 35 Dihedral angle restraints: 10275 sinusoidal: 4180 harmonic: 6095 Sorted by residual: dihedral pdb=" CA PHE B 89 " pdb=" C PHE B 89 " pdb=" N GLN B 90 " pdb=" CA GLN B 90 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE A 89 " pdb=" C PHE A 89 " pdb=" N GLN A 90 " pdb=" CA GLN A 90 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE C 89 " pdb=" C PHE C 89 " pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1350 0.028 - 0.057: 740 0.057 - 0.085: 270 0.085 - 0.114: 195 0.114 - 0.142: 40 Chirality restraints: 2595 Sorted by residual: chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE E 257 " pdb=" N ILE E 257 " pdb=" C ILE E 257 " pdb=" CB ILE E 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 257 " pdb=" N ILE C 257 " pdb=" C ILE C 257 " pdb=" CB ILE C 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2592 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 279 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 280 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 280 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 279 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 280 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO C 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " 0.026 5.00e-02 4.00e+02 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1473 2.72 - 3.27: 18501 3.27 - 3.81: 25600 3.81 - 4.36: 32484 4.36 - 4.90: 52739 Nonbonded interactions: 130797 Sorted by model distance: nonbonded pdb=" NZ LYS C 205 " pdb=" O ILE C 441 " model vdw 2.176 3.120 nonbonded pdb=" NZ LYS B 205 " pdb=" O ILE B 441 " model vdw 2.176 3.120 nonbonded pdb=" NZ LYS D 205 " pdb=" O ILE D 441 " model vdw 2.176 3.120 nonbonded pdb=" NZ LYS A 205 " pdb=" O ILE A 441 " model vdw 2.177 3.120 nonbonded pdb=" NZ LYS E 205 " pdb=" O ILE E 441 " model vdw 2.177 3.120 ... (remaining 130792 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' selection = chain 'E' } 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 group one per residue 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: 0.290 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.590 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.006 0.039 17040 Z= 0.378 Angle : 0.771 5.618 23175 Z= 0.425 Chirality : 0.046 0.142 2595 Planarity : 0.005 0.048 3015 Dihedral : 14.472 85.010 6325 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.74 % Allowed : 28.57 % Favored : 70.69 % Rotamer: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % 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: -6.49 (0.14), residues: 2030 helix: -5.04 (0.14), residues: 145 sheet: -5.28 (0.13), residues: 485 loop : -4.12 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 161 HIS 0.003 0.001 HIS B 86 PHE 0.010 0.001 PHE B 412 TYR 0.012 0.002 TYR D 55 ARG 0.002 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8811 (t0) cc_final: 0.8556 (t0) REVERT: A 146 MET cc_start: 0.8487 (ttt) cc_final: 0.7449 (ttm) REVERT: B 117 TRP cc_start: 0.9447 (m100) cc_final: 0.9217 (m100) REVERT: B 146 MET cc_start: 0.8517 (ttt) cc_final: 0.8028 (ttm) REVERT: B 171 TYR cc_start: 0.9149 (m-10) cc_final: 0.8890 (m-80) REVERT: B 239 LEU cc_start: 0.8801 (tp) cc_final: 0.8418 (tp) REVERT: C 63 ASP cc_start: 0.8618 (t0) cc_final: 0.8266 (t0) REVERT: C 146 MET cc_start: 0.8373 (ttt) cc_final: 0.7577 (ttm) REVERT: C 239 LEU cc_start: 0.9006 (tp) cc_final: 0.8547 (tp) REVERT: D 63 ASP cc_start: 0.8710 (t0) cc_final: 0.8367 (t0) REVERT: D 64 THR cc_start: 0.9310 (p) cc_final: 0.9098 (t) REVERT: D 81 ASN cc_start: 0.8888 (t0) cc_final: 0.8667 (t0) REVERT: D 125 LEU cc_start: 0.9137 (tp) cc_final: 0.8930 (tp) REVERT: D 133 ASN cc_start: 0.9393 (p0) cc_final: 0.9097 (p0) REVERT: D 146 MET cc_start: 0.8493 (ttt) cc_final: 0.7757 (ttm) REVERT: D 239 LEU cc_start: 0.8752 (tp) cc_final: 0.8281 (tp) REVERT: D 484 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7618 (mtm180) REVERT: E 116 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8618 (tpt90) REVERT: E 133 ASN cc_start: 0.9425 (p0) cc_final: 0.9175 (p0) REVERT: E 146 MET cc_start: 0.8646 (ttt) cc_final: 0.8149 (ttm) REVERT: E 317 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7968 (mm-30) REVERT: E 455 GLU cc_start: 0.8634 (tp30) cc_final: 0.8331 (mm-30) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2867 time to fit residues: 155.6238 Evaluate side-chains 233 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN B 329 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17040 Z= 0.269 Angle : 0.787 7.540 23175 Z= 0.397 Chirality : 0.048 0.186 2595 Planarity : 0.005 0.043 3015 Dihedral : 6.907 28.196 2265 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.59 % Favored : 82.17 % Rotamer: Outliers : 2.99 % Allowed : 18.88 % Favored : 78.13 % 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: -5.59 (0.15), residues: 2030 helix: -3.60 (0.34), residues: 155 sheet: -4.64 (0.16), residues: 465 loop : -3.62 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 215 HIS 0.007 0.001 HIS D 86 PHE 0.011 0.001 PHE D 344 TYR 0.021 0.002 TYR D 82 ARG 0.003 0.000 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 323 time to evaluate : 1.824 Fit side-chains REVERT: A 63 ASP cc_start: 0.8676 (t0) cc_final: 0.8429 (t0) REVERT: A 146 MET cc_start: 0.8192 (ttt) cc_final: 0.7810 (ttm) REVERT: A 148 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7473 (mt-10) REVERT: A 201 ASP cc_start: 0.8146 (t0) cc_final: 0.7575 (t0) REVERT: A 223 MET cc_start: 0.8653 (mmp) cc_final: 0.8242 (mmm) REVERT: B 117 TRP cc_start: 0.9430 (m100) cc_final: 0.9197 (m100) REVERT: B 122 LYS cc_start: 0.8810 (mttp) cc_final: 0.8248 (mtpp) REVERT: B 134 GLU cc_start: 0.7288 (pm20) cc_final: 0.6970 (pm20) REVERT: B 146 MET cc_start: 0.8183 (ttt) cc_final: 0.7459 (ttm) REVERT: B 168 GLU cc_start: 0.7729 (mp0) cc_final: 0.6784 (mp0) REVERT: B 171 TYR cc_start: 0.8826 (m-10) cc_final: 0.8585 (m-80) REVERT: B 201 ASP cc_start: 0.8446 (t0) cc_final: 0.7518 (t0) REVERT: B 289 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 383 GLN cc_start: 0.7441 (tp40) cc_final: 0.6978 (tp40) REVERT: C 68 TYR cc_start: 0.8885 (m-80) cc_final: 0.8543 (m-10) REVERT: C 146 MET cc_start: 0.8193 (ttt) cc_final: 0.7404 (ttm) REVERT: C 201 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7734 (t70) REVERT: C 227 TYR cc_start: 0.8971 (m-80) cc_final: 0.8574 (m-80) REVERT: C 327 SER cc_start: 0.9172 (m) cc_final: 0.8778 (t) REVERT: C 380 ASP cc_start: 0.7975 (t0) cc_final: 0.7649 (t0) REVERT: D 63 ASP cc_start: 0.8653 (t0) cc_final: 0.8252 (t0) REVERT: D 64 THR cc_start: 0.9343 (p) cc_final: 0.9089 (t) REVERT: D 81 ASN cc_start: 0.8552 (t0) cc_final: 0.8317 (t0) REVERT: D 116 ARG cc_start: 0.8777 (tpt170) cc_final: 0.8484 (tpt90) REVERT: D 133 ASN cc_start: 0.9325 (p0) cc_final: 0.8989 (p0) REVERT: D 146 MET cc_start: 0.8196 (ttt) cc_final: 0.7485 (ttm) REVERT: D 171 TYR cc_start: 0.8832 (m-10) cc_final: 0.8603 (m-10) REVERT: D 178 ASP cc_start: 0.8641 (t0) cc_final: 0.8348 (t0) REVERT: D 201 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7448 (t70) REVERT: D 284 ASP cc_start: 0.8427 (t0) cc_final: 0.7846 (t0) REVERT: D 484 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7342 (mtm180) REVERT: E 116 ARG cc_start: 0.8868 (tpt170) cc_final: 0.8607 (tpt170) REVERT: E 133 ASN cc_start: 0.9404 (p0) cc_final: 0.9126 (p0) REVERT: E 146 MET cc_start: 0.8386 (ttt) cc_final: 0.7909 (ttm) REVERT: E 168 GLU cc_start: 0.7649 (mp0) cc_final: 0.7422 (mp0) REVERT: E 201 ASP cc_start: 0.8395 (t0) cc_final: 0.7489 (t0) REVERT: E 223 MET cc_start: 0.8533 (mmp) cc_final: 0.8259 (mmm) REVERT: E 383 GLN cc_start: 0.7631 (tp40) cc_final: 0.7243 (tp40) REVERT: E 455 GLU cc_start: 0.8544 (tp30) cc_final: 0.8210 (mm-30) REVERT: E 460 LEU cc_start: 0.8804 (tt) cc_final: 0.8597 (tt) outliers start: 56 outliers final: 34 residues processed: 353 average time/residue: 0.2439 time to fit residues: 136.4019 Evaluate side-chains 302 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 329 ASN C 333 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 333 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17040 Z= 0.205 Angle : 0.731 8.445 23175 Z= 0.363 Chirality : 0.047 0.216 2595 Planarity : 0.005 0.038 3015 Dihedral : 6.170 27.278 2265 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.49 % Favored : 82.51 % Rotamer: Outliers : 5.40 % Allowed : 19.57 % Favored : 75.03 % 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: -5.19 (0.16), residues: 2030 helix: -3.31 (0.30), residues: 185 sheet: -4.22 (0.18), residues: 465 loop : -3.38 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 215 HIS 0.010 0.001 HIS B 492 PHE 0.009 0.001 PHE D 412 TYR 0.030 0.002 TYR B 227 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 317 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8054 (ttt) cc_final: 0.7325 (ttm) REVERT: A 148 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 201 ASP cc_start: 0.8141 (t0) cc_final: 0.7170 (t0) REVERT: A 223 MET cc_start: 0.8639 (mmp) cc_final: 0.8265 (mmm) REVERT: A 444 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8634 (ttt-90) REVERT: B 146 MET cc_start: 0.8119 (ttt) cc_final: 0.7479 (ttm) REVERT: B 171 TYR cc_start: 0.8690 (m-10) cc_final: 0.8380 (m-10) REVERT: B 201 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7688 (t0) REVERT: B 223 MET cc_start: 0.8642 (mmm) cc_final: 0.8293 (mmm) REVERT: B 289 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 146 MET cc_start: 0.8114 (ttt) cc_final: 0.7574 (ttm) REVERT: C 171 TYR cc_start: 0.8586 (m-10) cc_final: 0.8252 (m-10) REVERT: C 201 ASP cc_start: 0.8185 (t0) cc_final: 0.7716 (t0) REVERT: C 227 TYR cc_start: 0.8897 (m-80) cc_final: 0.8525 (m-80) REVERT: C 251 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 327 SER cc_start: 0.9162 (m) cc_final: 0.8844 (t) REVERT: C 380 ASP cc_start: 0.7840 (t0) cc_final: 0.7550 (t0) REVERT: D 133 ASN cc_start: 0.9218 (p0) cc_final: 0.8990 (p0) REVERT: D 146 MET cc_start: 0.8266 (ttt) cc_final: 0.7516 (ttm) REVERT: D 171 TYR cc_start: 0.8752 (m-10) cc_final: 0.8483 (m-10) REVERT: D 201 ASP cc_start: 0.8240 (t0) cc_final: 0.7422 (t0) REVERT: D 223 MET cc_start: 0.8831 (mmm) cc_final: 0.8561 (mmm) REVERT: D 284 ASP cc_start: 0.8338 (t0) cc_final: 0.7983 (t0) REVERT: D 484 ARG cc_start: 0.7461 (mtm180) cc_final: 0.7199 (mtm180) REVERT: E 133 ASN cc_start: 0.9417 (p0) cc_final: 0.9130 (p0) REVERT: E 146 MET cc_start: 0.8182 (ttt) cc_final: 0.7554 (ttm) REVERT: E 168 GLU cc_start: 0.7669 (mp0) cc_final: 0.7416 (mp0) REVERT: E 171 TYR cc_start: 0.8594 (m-10) cc_final: 0.8206 (m-10) REVERT: E 201 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7632 (t0) outliers start: 101 outliers final: 58 residues processed: 387 average time/residue: 0.2461 time to fit residues: 149.8206 Evaluate side-chains 327 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 266 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 177 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17040 Z= 0.368 Angle : 0.777 9.065 23175 Z= 0.389 Chirality : 0.048 0.214 2595 Planarity : 0.005 0.042 3015 Dihedral : 6.392 27.571 2265 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.19 % Favored : 82.81 % Rotamer: Outliers : 7.22 % Allowed : 19.04 % Favored : 73.74 % 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: -5.04 (0.16), residues: 2030 helix: -3.19 (0.29), residues: 185 sheet: -4.13 (0.18), residues: 465 loop : -3.27 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 215 HIS 0.010 0.002 HIS B 492 PHE 0.014 0.001 PHE D 232 TYR 0.026 0.002 TYR C 82 ARG 0.004 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 277 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7324 (mt-10) REVERT: A 223 MET cc_start: 0.8805 (mmp) cc_final: 0.8447 (mmm) REVERT: A 251 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8885 (tt) REVERT: A 362 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7673 (tp) REVERT: B 146 MET cc_start: 0.8211 (ttt) cc_final: 0.7363 (ttm) REVERT: B 201 ASP cc_start: 0.8370 (t0) cc_final: 0.7649 (t70) REVERT: B 289 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 362 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7648 (tp) REVERT: C 71 ASP cc_start: 0.7294 (t70) cc_final: 0.6634 (t70) REVERT: C 146 MET cc_start: 0.8177 (ttt) cc_final: 0.7674 (ttm) REVERT: C 201 ASP cc_start: 0.8253 (t0) cc_final: 0.7940 (t0) REVERT: C 251 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8749 (tt) REVERT: C 327 SER cc_start: 0.9173 (m) cc_final: 0.8779 (t) REVERT: D 68 TYR cc_start: 0.8875 (m-80) cc_final: 0.8555 (m-10) REVERT: D 133 ASN cc_start: 0.9320 (p0) cc_final: 0.8966 (p0) REVERT: D 146 MET cc_start: 0.8289 (ttt) cc_final: 0.7659 (ttm) REVERT: D 171 TYR cc_start: 0.8967 (m-10) cc_final: 0.8674 (m-10) REVERT: D 201 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7672 (t0) REVERT: D 223 MET cc_start: 0.8928 (mmm) cc_final: 0.8698 (mmm) REVERT: D 362 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7407 (tp) REVERT: D 380 ASP cc_start: 0.8509 (t0) cc_final: 0.8243 (t0) REVERT: D 484 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7090 (mtm180) REVERT: E 133 ASN cc_start: 0.9331 (p0) cc_final: 0.9125 (p0) REVERT: E 146 MET cc_start: 0.8270 (ttt) cc_final: 0.7283 (ttm) REVERT: E 171 TYR cc_start: 0.8743 (m-10) cc_final: 0.8500 (m-10) REVERT: E 201 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7427 (t0) REVERT: E 289 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7456 (mt-10) outliers start: 135 outliers final: 89 residues processed: 369 average time/residue: 0.2347 time to fit residues: 138.9587 Evaluate side-chains 349 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 253 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 466 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17040 Z= 0.324 Angle : 0.766 7.907 23175 Z= 0.382 Chirality : 0.047 0.172 2595 Planarity : 0.005 0.041 3015 Dihedral : 6.383 27.216 2265 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.34 % Favored : 82.66 % Rotamer: Outliers : 6.42 % Allowed : 20.91 % Favored : 72.67 % 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: -4.90 (0.17), residues: 2030 helix: -2.99 (0.30), residues: 185 sheet: -3.99 (0.19), residues: 465 loop : -3.20 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 376 HIS 0.010 0.002 HIS B 492 PHE 0.009 0.001 PHE E 412 TYR 0.026 0.002 TYR A 62 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 281 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 171 TYR cc_start: 0.8791 (m-80) cc_final: 0.8526 (m-80) REVERT: A 198 LEU cc_start: 0.8332 (pt) cc_final: 0.8100 (mp) REVERT: A 223 MET cc_start: 0.8795 (mmp) cc_final: 0.8436 (mmm) REVERT: A 251 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8893 (tt) REVERT: A 476 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7247 (mm110) REVERT: B 71 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7928 (t70) REVERT: B 146 MET cc_start: 0.8197 (ttt) cc_final: 0.7420 (ttm) REVERT: B 171 TYR cc_start: 0.8647 (m-80) cc_final: 0.8346 (m-10) REVERT: B 201 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7730 (t70) REVERT: B 289 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7613 (mt-10) REVERT: C 71 ASP cc_start: 0.7443 (t70) cc_final: 0.6758 (t70) REVERT: C 146 MET cc_start: 0.8131 (ttt) cc_final: 0.7725 (ttm) REVERT: C 171 TYR cc_start: 0.8753 (m-10) cc_final: 0.8511 (m-10) REVERT: C 251 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (tt) REVERT: C 327 SER cc_start: 0.9153 (m) cc_final: 0.8866 (t) REVERT: C 380 ASP cc_start: 0.7963 (t0) cc_final: 0.7762 (t0) REVERT: D 61 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7556 (pt) REVERT: D 68 TYR cc_start: 0.8849 (m-80) cc_final: 0.8606 (m-10) REVERT: D 133 ASN cc_start: 0.9212 (p0) cc_final: 0.8915 (p0) REVERT: D 146 MET cc_start: 0.8239 (ttt) cc_final: 0.7440 (ttm) REVERT: D 171 TYR cc_start: 0.8966 (m-10) cc_final: 0.8718 (m-10) REVERT: D 178 ASP cc_start: 0.8626 (t0) cc_final: 0.8177 (t0) REVERT: D 201 ASP cc_start: 0.8290 (t0) cc_final: 0.7429 (t70) REVERT: D 380 ASP cc_start: 0.8596 (t0) cc_final: 0.8282 (t0) REVERT: D 466 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (pt) REVERT: E 68 TYR cc_start: 0.8744 (m-80) cc_final: 0.8524 (m-80) REVERT: E 146 MET cc_start: 0.8244 (ttt) cc_final: 0.7382 (ttm) REVERT: E 201 ASP cc_start: 0.8256 (t0) cc_final: 0.7615 (t0) REVERT: E 289 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7420 (mt-10) REVERT: E 380 ASP cc_start: 0.8229 (t0) cc_final: 0.7996 (t0) REVERT: E 397 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8362 (m-80) outliers start: 120 outliers final: 92 residues processed: 368 average time/residue: 0.2317 time to fit residues: 136.8669 Evaluate side-chains 347 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 248 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 397 TYR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 181 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 181 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17040 Z= 0.204 Angle : 0.734 13.892 23175 Z= 0.360 Chirality : 0.045 0.152 2595 Planarity : 0.005 0.042 3015 Dihedral : 6.046 25.840 2265 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 6.10 % Allowed : 22.89 % Favored : 71.02 % 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: -4.65 (0.17), residues: 2030 helix: -2.51 (0.32), residues: 185 sheet: -3.80 (0.20), residues: 465 loop : -3.09 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.010 0.001 HIS B 492 PHE 0.008 0.001 PHE E 412 TYR 0.025 0.002 TYR B 62 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 299 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7061 (mt-10) REVERT: A 171 TYR cc_start: 0.8630 (m-80) cc_final: 0.8270 (m-80) REVERT: A 223 MET cc_start: 0.8731 (mmp) cc_final: 0.8337 (mmm) REVERT: A 327 SER cc_start: 0.8844 (m) cc_final: 0.8399 (t) REVERT: A 362 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 476 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7202 (mm-40) REVERT: B 71 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8005 (t70) REVERT: B 146 MET cc_start: 0.7987 (ttt) cc_final: 0.7148 (ttt) REVERT: B 171 TYR cc_start: 0.8584 (m-80) cc_final: 0.8269 (m-80) REVERT: B 201 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7855 (t0) REVERT: C 61 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7539 (pt) REVERT: C 146 MET cc_start: 0.8029 (ttt) cc_final: 0.7446 (ttm) REVERT: C 171 TYR cc_start: 0.8622 (m-10) cc_final: 0.8261 (m-10) REVERT: C 201 ASP cc_start: 0.8056 (t0) cc_final: 0.7189 (t0) REVERT: C 223 MET cc_start: 0.8550 (mmm) cc_final: 0.8337 (mmm) REVERT: C 227 TYR cc_start: 0.8907 (m-80) cc_final: 0.8672 (m-80) REVERT: C 251 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 327 SER cc_start: 0.9114 (m) cc_final: 0.8846 (t) REVERT: C 476 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7522 (mm110) REVERT: D 146 MET cc_start: 0.8123 (ttt) cc_final: 0.7470 (ttm) REVERT: D 171 TYR cc_start: 0.8875 (m-10) cc_final: 0.8634 (m-80) REVERT: D 201 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7779 (t0) REVERT: D 223 MET cc_start: 0.8674 (mmm) cc_final: 0.8417 (mmm) REVERT: D 343 TRP cc_start: 0.8936 (t60) cc_final: 0.8594 (t60) REVERT: D 362 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7450 (tp) REVERT: E 68 TYR cc_start: 0.8617 (m-80) cc_final: 0.8324 (m-80) REVERT: E 146 MET cc_start: 0.8148 (ttt) cc_final: 0.7477 (ttm) REVERT: E 201 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7602 (t0) REVERT: E 223 MET cc_start: 0.8593 (mmm) cc_final: 0.8129 (mmm) REVERT: E 289 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7347 (mt-10) REVERT: E 343 TRP cc_start: 0.8907 (t60) cc_final: 0.8575 (t60) REVERT: E 380 ASP cc_start: 0.8106 (t0) cc_final: 0.7862 (t0) outliers start: 114 outliers final: 76 residues processed: 377 average time/residue: 0.2497 time to fit residues: 147.8997 Evaluate side-chains 352 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 268 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17040 Z= 0.230 Angle : 0.734 13.403 23175 Z= 0.361 Chirality : 0.045 0.169 2595 Planarity : 0.005 0.050 3015 Dihedral : 5.970 25.566 2265 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 5.51 % Allowed : 24.33 % Favored : 70.16 % 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: -4.50 (0.17), residues: 2030 helix: -2.09 (0.34), residues: 185 sheet: -3.65 (0.20), residues: 465 loop : -3.05 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 343 HIS 0.010 0.001 HIS B 492 PHE 0.008 0.001 PHE A 433 TYR 0.026 0.002 TYR A 62 ARG 0.004 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 288 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7474 (pt) REVERT: A 148 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7041 (mt-10) REVERT: A 171 TYR cc_start: 0.8551 (m-80) cc_final: 0.8254 (m-80) REVERT: A 223 MET cc_start: 0.8736 (mmp) cc_final: 0.8324 (mmm) REVERT: A 327 SER cc_start: 0.8827 (m) cc_final: 0.8451 (t) REVERT: A 362 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7379 (tp) REVERT: A 476 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7269 (mm-40) REVERT: B 71 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7963 (t70) REVERT: B 146 MET cc_start: 0.8027 (ttt) cc_final: 0.7121 (ttt) REVERT: B 171 TYR cc_start: 0.8668 (m-80) cc_final: 0.8447 (m-80) REVERT: B 201 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7960 (t0) REVERT: B 362 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (tp) REVERT: C 71 ASP cc_start: 0.7414 (t70) cc_final: 0.6683 (t70) REVERT: C 146 MET cc_start: 0.7967 (ttt) cc_final: 0.7579 (ttm) REVERT: C 201 ASP cc_start: 0.8097 (t0) cc_final: 0.7232 (t0) REVERT: C 251 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8716 (tt) REVERT: C 327 SER cc_start: 0.9099 (m) cc_final: 0.8829 (t) REVERT: D 146 MET cc_start: 0.8138 (ttt) cc_final: 0.7524 (ttm) REVERT: D 171 TYR cc_start: 0.8975 (m-10) cc_final: 0.8704 (m-10) REVERT: D 201 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7845 (t0) REVERT: D 484 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7234 (mtm180) REVERT: E 68 TYR cc_start: 0.8619 (m-80) cc_final: 0.8380 (m-80) REVERT: E 146 MET cc_start: 0.8156 (ttt) cc_final: 0.7222 (ttm) REVERT: E 201 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7436 (t0) REVERT: E 289 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7302 (mt-10) REVERT: E 380 ASP cc_start: 0.8162 (t0) cc_final: 0.7913 (t0) outliers start: 103 outliers final: 79 residues processed: 359 average time/residue: 0.2312 time to fit residues: 133.1772 Evaluate side-chains 360 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 273 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 125 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 181 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17040 Z= 0.284 Angle : 0.750 12.592 23175 Z= 0.370 Chirality : 0.046 0.177 2595 Planarity : 0.005 0.061 3015 Dihedral : 6.066 25.678 2265 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer: Outliers : 5.78 % Allowed : 23.80 % Favored : 70.43 % 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: -4.36 (0.17), residues: 2030 helix: -1.89 (0.35), residues: 185 sheet: -3.48 (0.21), residues: 465 loop : -3.00 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 343 HIS 0.009 0.001 HIS B 492 PHE 0.012 0.001 PHE C 232 TYR 0.028 0.002 TYR C 227 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 281 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7537 (pt) REVERT: A 148 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7024 (mt-10) REVERT: A 171 TYR cc_start: 0.8678 (m-80) cc_final: 0.8406 (m-80) REVERT: A 223 MET cc_start: 0.8761 (mmp) cc_final: 0.8314 (mmm) REVERT: A 327 SER cc_start: 0.8828 (m) cc_final: 0.8387 (t) REVERT: A 362 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7369 (tp) REVERT: B 71 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7854 (t70) REVERT: B 146 MET cc_start: 0.8046 (ttt) cc_final: 0.7200 (ttt) REVERT: B 171 TYR cc_start: 0.8714 (m-80) cc_final: 0.8472 (m-80) REVERT: B 201 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8042 (t0) REVERT: C 146 MET cc_start: 0.7897 (ttt) cc_final: 0.7613 (ttm) REVERT: C 171 TYR cc_start: 0.8673 (m-10) cc_final: 0.8252 (m-10) REVERT: C 223 MET cc_start: 0.8478 (mmm) cc_final: 0.8045 (mmm) REVERT: C 251 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8746 (tt) REVERT: C 327 SER cc_start: 0.9098 (m) cc_final: 0.8839 (t) REVERT: D 146 MET cc_start: 0.8162 (ttt) cc_final: 0.7560 (ttm) REVERT: D 171 TYR cc_start: 0.8994 (m-10) cc_final: 0.8761 (m-10) REVERT: D 201 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7926 (t70) REVERT: D 223 MET cc_start: 0.8713 (mmm) cc_final: 0.8345 (mmm) REVERT: D 376 TRP cc_start: 0.8579 (t-100) cc_final: 0.8308 (m-90) REVERT: D 484 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7247 (mtm180) REVERT: E 68 TYR cc_start: 0.8701 (m-80) cc_final: 0.8476 (m-80) REVERT: E 146 MET cc_start: 0.8171 (ttt) cc_final: 0.7303 (ttm) REVERT: E 201 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7586 (t0) REVERT: E 223 MET cc_start: 0.8378 (mmm) cc_final: 0.7890 (mmm) REVERT: E 289 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 380 ASP cc_start: 0.8260 (t0) cc_final: 0.8007 (t0) outliers start: 108 outliers final: 91 residues processed: 353 average time/residue: 0.2299 time to fit residues: 130.9714 Evaluate side-chains 364 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 266 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17040 Z= 0.281 Angle : 0.761 12.743 23175 Z= 0.373 Chirality : 0.047 0.222 2595 Planarity : 0.005 0.059 3015 Dihedral : 6.095 25.826 2265 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 5.67 % Allowed : 24.55 % Favored : 69.79 % 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: -4.36 (0.17), residues: 2030 helix: -1.71 (0.36), residues: 185 sheet: -3.48 (0.21), residues: 485 loop : -3.01 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 343 HIS 0.011 0.001 HIS B 492 PHE 0.014 0.001 PHE A 141 TYR 0.029 0.002 TYR C 227 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 268 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7390 (pt) REVERT: A 95 GLN cc_start: 0.6936 (mt0) cc_final: 0.6731 (mt0) REVERT: A 148 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6999 (mt-10) REVERT: A 223 MET cc_start: 0.8769 (mmp) cc_final: 0.8424 (mmm) REVERT: A 327 SER cc_start: 0.8826 (m) cc_final: 0.8416 (t) REVERT: A 362 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7315 (tp) REVERT: A 380 ASP cc_start: 0.8307 (t0) cc_final: 0.8072 (t0) REVERT: B 71 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7836 (t70) REVERT: B 146 MET cc_start: 0.8052 (ttt) cc_final: 0.7251 (ttt) REVERT: B 168 GLU cc_start: 0.7572 (mp0) cc_final: 0.7287 (pm20) REVERT: B 171 TYR cc_start: 0.8749 (m-80) cc_final: 0.8530 (m-80) REVERT: B 201 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8062 (t0) REVERT: B 380 ASP cc_start: 0.8308 (t70) cc_final: 0.7744 (m-30) REVERT: C 223 MET cc_start: 0.8581 (mmm) cc_final: 0.8311 (mmm) REVERT: C 327 SER cc_start: 0.9105 (m) cc_final: 0.8792 (t) REVERT: D 146 MET cc_start: 0.8150 (ttt) cc_final: 0.7604 (ttm) REVERT: D 171 TYR cc_start: 0.9012 (m-10) cc_final: 0.8780 (m-10) REVERT: D 201 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7950 (t70) REVERT: D 223 MET cc_start: 0.8779 (mmm) cc_final: 0.8427 (mmm) REVERT: D 484 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7218 (mtm180) REVERT: E 146 MET cc_start: 0.8156 (ttt) cc_final: 0.7318 (ttm) REVERT: E 201 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7635 (t0) REVERT: E 380 ASP cc_start: 0.8285 (t0) cc_final: 0.8012 (t0) outliers start: 106 outliers final: 95 residues processed: 340 average time/residue: 0.2269 time to fit residues: 124.8785 Evaluate side-chains 362 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 261 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17040 Z= 0.358 Angle : 0.796 12.289 23175 Z= 0.394 Chirality : 0.049 0.336 2595 Planarity : 0.005 0.060 3015 Dihedral : 6.323 26.388 2265 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.90 % Favored : 83.10 % Rotamer: Outliers : 5.83 % Allowed : 24.65 % Favored : 69.52 % 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: -4.42 (0.17), residues: 2030 helix: -1.81 (0.36), residues: 185 sheet: -3.51 (0.21), residues: 485 loop : -3.05 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 343 HIS 0.011 0.002 HIS B 492 PHE 0.013 0.001 PHE A 141 TYR 0.030 0.002 TYR A 62 ARG 0.004 0.000 ARG E 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 259 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 223 MET cc_start: 0.8823 (mmp) cc_final: 0.8455 (mmm) REVERT: A 327 SER cc_start: 0.8870 (m) cc_final: 0.8417 (t) REVERT: A 362 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7549 (tp) REVERT: A 380 ASP cc_start: 0.8406 (t0) cc_final: 0.8202 (t0) REVERT: B 71 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8130 (t70) REVERT: B 146 MET cc_start: 0.8001 (ttt) cc_final: 0.7485 (ttt) REVERT: B 168 GLU cc_start: 0.7634 (mp0) cc_final: 0.7398 (pm20) REVERT: B 171 TYR cc_start: 0.8753 (m-80) cc_final: 0.8513 (m-80) REVERT: B 201 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8189 (t70) REVERT: C 53 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (pt) REVERT: C 327 SER cc_start: 0.9122 (m) cc_final: 0.8808 (t) REVERT: D 146 MET cc_start: 0.8166 (ttt) cc_final: 0.7577 (ttm) REVERT: D 201 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7942 (t70) REVERT: D 223 MET cc_start: 0.8836 (mmm) cc_final: 0.8430 (mmm) REVERT: D 484 ARG cc_start: 0.7520 (mtm180) cc_final: 0.7203 (mtm180) REVERT: E 146 MET cc_start: 0.8186 (ttt) cc_final: 0.7407 (ttm) REVERT: E 178 ASP cc_start: 0.8481 (t0) cc_final: 0.8162 (t0) REVERT: E 201 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7833 (t0) REVERT: E 380 ASP cc_start: 0.8357 (t0) cc_final: 0.8065 (t0) outliers start: 109 outliers final: 93 residues processed: 335 average time/residue: 0.2412 time to fit residues: 130.3990 Evaluate side-chains 349 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 250 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 396 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103487 restraints weight = 28359.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106794 restraints weight = 14305.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108960 restraints weight = 8730.871| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17040 Z= 0.194 Angle : 0.748 12.527 23175 Z= 0.364 Chirality : 0.047 0.276 2595 Planarity : 0.005 0.059 3015 Dihedral : 5.983 25.623 2265 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 4.65 % Allowed : 25.88 % Favored : 69.47 % 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: -4.30 (0.17), residues: 2030 helix: -1.52 (0.37), residues: 185 sheet: -3.39 (0.20), residues: 495 loop : -3.01 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 359 HIS 0.011 0.001 HIS B 492 PHE 0.011 0.001 PHE C 232 TYR 0.027 0.002 TYR A 62 ARG 0.004 0.000 ARG E 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.66 seconds wall clock time: 59 minutes 44.63 seconds (3584.63 seconds total)