Starting phenix.real_space_refine on Sun Apr 7 16:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy9_33514/04_2024/7xy9_33514.pdb" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.110 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 8 5.21 5 S 72 5.16 5 C 6640 2.51 5 N 1808 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ASP 247": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10962 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 286 SG CYS A 37 70.821 60.293 24.390 1.00 40.90 S ATOM 2132 SG CYS A 295 64.935 51.850 36.905 1.00 39.55 S ATOM 4726 SG CYS B 295 43.904 51.877 46.832 1.00 35.49 S ATOM 2880 SG CYS B 37 38.029 60.293 59.329 1.00 38.05 S ATOM 7320 SG CYS C 295 65.020 30.263 46.889 1.00 36.74 S ATOM 5474 SG CYS C 37 70.759 21.742 59.360 1.00 40.13 S ATOM 9914 SG CYS D 295 43.871 30.247 36.849 1.00 37.58 S ATOM 8068 SG CYS D 37 38.064 21.769 24.366 1.00 40.89 S Time building chain proxies: 6.58, per 1000 atoms: 0.60 Number of scatterers: 10962 At special positions: 0 Unit cell: (109.699, 82.9026, 84.5774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 72 16.00 Mg 8 11.99 O 2430 8.00 N 1808 7.00 C 6640 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 59 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 59 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 37 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 37 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 59 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 37 " 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 35.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.601A pdb=" N ILE A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.708A pdb=" N GLY A 221 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.924A pdb=" N MET A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.925A pdb=" N LYS A 318 " --> pdb=" O ASP A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.588A pdb=" N ILE B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.726A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.584A pdb=" N MET B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.931A pdb=" N LYS B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.629A pdb=" N ILE C 41 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 217 through 221 removed outlier: 3.702A pdb=" N GLY C 221 " --> pdb=" O TYR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.912A pdb=" N MET C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.942A pdb=" N LYS C 318 " --> pdb=" O ASP C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.592A pdb=" N ILE D 41 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 150 through 162 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 200 through 211 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.921A pdb=" N MET D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 315 through 318 removed outlier: 3.960A pdb=" N LYS D 318 " --> pdb=" O ASP D 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 315 through 318' Processing helix chain 'D' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.544A pdb=" N LYS A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.598A pdb=" N ILE A 28 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 62 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 61 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 83 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.355A pdb=" N VAL A 320 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 348 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS A 322 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 350 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 324 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 216 removed outlier: 8.908A pdb=" N ASP A 237 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 261 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ASP B 237 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 261 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE B 28 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 62 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA B 61 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 83 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 4.344A pdb=" N VAL B 320 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 348 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 322 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 350 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 324 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.574A pdb=" N LYS C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE C 28 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 62 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA C 61 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.378A pdb=" N VAL C 320 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 348 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 322 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 350 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 324 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 214 through 216 removed outlier: 8.902A pdb=" N ASP C 237 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 261 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ASP D 237 " --> pdb=" O GLY D 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 261 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.566A pdb=" N LYS D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.520A pdb=" N ILE D 28 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 62 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 61 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.336A pdb=" N VAL D 320 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 348 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS D 322 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE D 350 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE D 324 " --> pdb=" O ILE D 350 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1203 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: 3.74 Time building geometry restraints manager: 4.96 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: 3426 1.34 - 1.46: 2195 1.46 - 1.58: 4859 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 10608 Sorted by residual: bond pdb=" C CYS D 295 " pdb=" N PRO D 296 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.01e-02 9.80e+03 1.32e+00 bond pdb=" C CYS C 295 " pdb=" N PRO C 296 " ideal model delta sigma weight residual 1.333 1.345 -0.011 1.01e-02 9.80e+03 1.19e+00 bond pdb=" N CYS D 295 " pdb=" CA CYS D 295 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 9.23e-01 bond pdb=" C LEU D 294 " pdb=" N CYS D 295 " ideal model delta sigma weight residual 1.341 1.327 0.013 1.65e-02 3.67e+03 6.53e-01 bond pdb=" CA TYR D 218 " pdb=" CB TYR D 218 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 ... (remaining 10603 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 423 107.08 - 113.80: 5923 113.80 - 120.53: 3877 120.53 - 127.25: 3986 127.25 - 133.98: 135 Bond angle restraints: 14344 Sorted by residual: angle pdb=" CG1 ILE A 175 " pdb=" CB ILE A 175 " pdb=" CG2 ILE A 175 " ideal model delta sigma weight residual 110.70 100.70 10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N LEU B 294 " pdb=" CA LEU B 294 " pdb=" C LEU B 294 " ideal model delta sigma weight residual 110.65 106.59 4.06 1.26e+00 6.30e-01 1.04e+01 angle pdb=" C MET B 147 " pdb=" N ILE B 148 " pdb=" CA ILE B 148 " ideal model delta sigma weight residual 120.33 122.90 -2.57 8.00e-01 1.56e+00 1.03e+01 angle pdb=" N LEU A 294 " pdb=" CA LEU A 294 " pdb=" C LEU A 294 " ideal model delta sigma weight residual 110.65 106.62 4.03 1.26e+00 6.30e-01 1.03e+01 angle pdb=" N PRO C 296 " pdb=" CA PRO C 296 " pdb=" C PRO C 296 " ideal model delta sigma weight residual 110.50 115.01 -4.51 1.57e+00 4.06e-01 8.25e+00 ... (remaining 14339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5471 17.42 - 34.84: 580 34.84 - 52.26: 168 52.26 - 69.68: 65 69.68 - 87.10: 24 Dihedral angle restraints: 6308 sinusoidal: 2492 harmonic: 3816 Sorted by residual: dihedral pdb=" CA CYS A 295 " pdb=" C CYS A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA CYS B 295 " pdb=" C CYS B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS D 295 " pdb=" C CYS D 295 " pdb=" N PRO D 296 " pdb=" CA PRO D 296 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1231 0.049 - 0.097: 258 0.097 - 0.146: 102 0.146 - 0.194: 0 0.194 - 0.243: 1 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 62 " pdb=" N VAL A 62 " pdb=" C VAL A 62 " pdb=" CB VAL A 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1589 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 200 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 201 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 200 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 201 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 200 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 201 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " 0.029 5.00e-02 4.00e+02 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 145 2.57 - 3.15: 8664 3.15 - 3.74: 18347 3.74 - 4.32: 27448 4.32 - 4.90: 42748 Nonbonded interactions: 97352 Sorted by model distance: nonbonded pdb=" OD2 ASP C 150 " pdb="ZN ZN C 503 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP D 150 " pdb="ZN ZN D 503 " model vdw 1.996 2.230 nonbonded pdb=" NE2 HIS A 157 " pdb="MG MG A 403 " model vdw 2.038 2.250 nonbonded pdb=" NE2 HIS B 157 " pdb="MG MG B 502 " model vdw 2.039 2.250 nonbonded pdb=" NE2 HIS C 157 " pdb="MG MG C 502 " model vdw 2.040 2.250 ... (remaining 97347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 351 or resid 402)) selection = (chain 'B' and (resid 0 through 351 or resid 502)) selection = (chain 'C' and (resid 0 through 351 or resid 502)) selection = (chain 'D' and (resid 0 through 351 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 6.390 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.880 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10608 Z= 0.152 Angle : 0.544 10.000 14344 Z= 0.292 Chirality : 0.046 0.243 1592 Planarity : 0.004 0.056 1856 Dihedral : 17.431 87.100 3884 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.67 % Allowed : 19.80 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1360 helix: 1.10 (0.25), residues: 452 sheet: 0.81 (0.31), residues: 304 loop : -0.56 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.004 0.001 HIS D 157 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR D 311 ARG 0.001 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.476 Fit side-chains REVERT: A 92 THR cc_start: 0.8827 (m) cc_final: 0.8521 (p) REVERT: C 340 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (ptmt) outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 1.6314 time to fit residues: 243.4725 Evaluate side-chains 141 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 10608 Z= 0.444 Angle : 0.761 9.263 14344 Z= 0.413 Chirality : 0.055 0.194 1592 Planarity : 0.006 0.064 1856 Dihedral : 8.181 59.977 1488 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.53 % Allowed : 16.73 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1360 helix: 0.52 (0.23), residues: 452 sheet: 0.24 (0.27), residues: 332 loop : -0.81 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 110 HIS 0.006 0.002 HIS A 157 PHE 0.016 0.002 PHE D 124 TYR 0.014 0.003 TYR B 311 ARG 0.006 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.618 Fit side-chains REVERT: A 92 THR cc_start: 0.8666 (m) cc_final: 0.8289 (p) REVERT: A 106 MET cc_start: 0.8341 (mmt) cc_final: 0.8081 (mmm) REVERT: A 335 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6116 (mpm) REVERT: C 335 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.6095 (mpm) REVERT: D 16 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7521 (tp30) outliers start: 38 outliers final: 22 residues processed: 164 average time/residue: 1.5368 time to fit residues: 268.9857 Evaluate side-chains 161 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 342 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10608 Z= 0.372 Angle : 0.711 9.171 14344 Z= 0.386 Chirality : 0.053 0.177 1592 Planarity : 0.006 0.065 1856 Dihedral : 7.921 59.828 1478 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.72 % Allowed : 15.80 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1360 helix: 0.43 (0.23), residues: 452 sheet: 0.10 (0.27), residues: 332 loop : -0.89 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 110 HIS 0.006 0.002 HIS D 157 PHE 0.015 0.002 PHE A 124 TYR 0.013 0.003 TYR A 311 ARG 0.005 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.200 Fit side-chains REVERT: A 0 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5165 (m-70) REVERT: A 92 THR cc_start: 0.8624 (m) cc_final: 0.8256 (p) REVERT: A 106 MET cc_start: 0.8342 (mmt) cc_final: 0.8029 (mmm) REVERT: A 335 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.6111 (mpm) REVERT: B 9 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7299 (tt) REVERT: C 138 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7795 (ptpp) REVERT: C 139 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: D 16 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: D 138 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7763 (ptpp) REVERT: D 294 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7520 (mt) outliers start: 40 outliers final: 21 residues processed: 162 average time/residue: 1.5696 time to fit residues: 271.4860 Evaluate side-chains 165 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 342 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10608 Z= 0.143 Angle : 0.533 9.160 14344 Z= 0.285 Chirality : 0.046 0.233 1592 Planarity : 0.004 0.057 1856 Dihedral : 6.884 58.481 1474 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.74 % 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: 0.09 (0.22), residues: 1360 helix: 0.99 (0.24), residues: 452 sheet: 0.54 (0.29), residues: 304 loop : -0.88 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.006 0.001 HIS D 157 PHE 0.009 0.001 PHE A 124 TYR 0.010 0.001 TYR D 311 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.227 Fit side-chains REVERT: A 92 THR cc_start: 0.8371 (m) cc_final: 0.8049 (p) REVERT: A 106 MET cc_start: 0.8202 (mmt) cc_final: 0.7953 (mmm) REVERT: B 106 MET cc_start: 0.8229 (mmt) cc_final: 0.7976 (mmm) REVERT: B 335 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7864 (mpm) REVERT: C 106 MET cc_start: 0.8207 (mmt) cc_final: 0.7924 (mmm) REVERT: C 335 MET cc_start: 0.8205 (mmp) cc_final: 0.7854 (mpm) REVERT: D 106 MET cc_start: 0.8247 (mmt) cc_final: 0.7959 (mmm) REVERT: D 139 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7111 (mt-10) outliers start: 29 outliers final: 11 residues processed: 150 average time/residue: 1.5340 time to fit residues: 245.7699 Evaluate side-chains 146 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10608 Z= 0.361 Angle : 0.690 9.545 14344 Z= 0.375 Chirality : 0.052 0.181 1592 Planarity : 0.006 0.063 1856 Dihedral : 7.068 59.013 1468 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.16 % Allowed : 16.73 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1360 helix: 0.61 (0.23), residues: 452 sheet: 0.08 (0.27), residues: 332 loop : -0.83 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 90 HIS 0.005 0.002 HIS A 102 PHE 0.015 0.002 PHE A 124 TYR 0.014 0.003 TYR A 311 ARG 0.005 0.001 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.254 Fit side-chains REVERT: A 0 HIS cc_start: 0.6210 (OUTLIER) cc_final: 0.5129 (m-70) REVERT: A 92 THR cc_start: 0.8562 (m) cc_final: 0.8197 (p) REVERT: A 106 MET cc_start: 0.8311 (mmt) cc_final: 0.8005 (mmm) REVERT: B 0 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5476 (m-70) REVERT: B 106 MET cc_start: 0.8270 (mmt) cc_final: 0.7987 (mmm) REVERT: B 335 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7868 (mpm) REVERT: C 138 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (ptpp) REVERT: D 138 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7700 (ptpp) REVERT: D 335 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6067 (mpm) outliers start: 34 outliers final: 15 residues processed: 159 average time/residue: 1.5602 time to fit residues: 264.6892 Evaluate side-chains 158 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 0 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 342 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10608 Z= 0.138 Angle : 0.531 9.556 14344 Z= 0.283 Chirality : 0.046 0.243 1592 Planarity : 0.004 0.059 1856 Dihedral : 6.419 59.897 1467 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.77 % Allowed : 18.49 % Favored : 79.74 % 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: 0.15 (0.22), residues: 1360 helix: 1.04 (0.24), residues: 452 sheet: 0.42 (0.28), residues: 328 loop : -0.80 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.006 0.001 HIS D 157 PHE 0.009 0.001 PHE A 124 TYR 0.009 0.001 TYR D 311 ARG 0.001 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.212 Fit side-chains REVERT: A 0 HIS cc_start: 0.6056 (OUTLIER) cc_final: 0.5034 (m-70) REVERT: A 92 THR cc_start: 0.8326 (m) cc_final: 0.7996 (p) REVERT: A 106 MET cc_start: 0.8246 (mmt) cc_final: 0.7989 (mmm) REVERT: A 335 MET cc_start: 0.8104 (mmp) cc_final: 0.7851 (mpm) REVERT: B 106 MET cc_start: 0.8193 (mmt) cc_final: 0.7915 (mmm) REVERT: B 335 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7840 (mpm) REVERT: C 106 MET cc_start: 0.8207 (mmt) cc_final: 0.7940 (mmm) REVERT: C 335 MET cc_start: 0.8169 (mmp) cc_final: 0.7859 (mpm) REVERT: D 106 MET cc_start: 0.8230 (mmt) cc_final: 0.7955 (mmm) outliers start: 19 outliers final: 8 residues processed: 152 average time/residue: 1.6137 time to fit residues: 260.9754 Evaluate side-chains 143 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10608 Z= 0.156 Angle : 0.542 9.797 14344 Z= 0.289 Chirality : 0.046 0.235 1592 Planarity : 0.004 0.057 1856 Dihedral : 6.275 59.189 1467 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 18.87 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1360 helix: 1.12 (0.25), residues: 452 sheet: 0.54 (0.28), residues: 328 loop : -0.77 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.004 0.001 HIS D 157 PHE 0.010 0.001 PHE A 124 TYR 0.010 0.001 TYR D 311 ARG 0.001 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.247 Fit side-chains REVERT: A 92 THR cc_start: 0.8334 (m) cc_final: 0.7980 (p) REVERT: A 106 MET cc_start: 0.8234 (mmt) cc_final: 0.7955 (mmm) REVERT: A 335 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7881 (mpm) REVERT: B 106 MET cc_start: 0.8211 (mmt) cc_final: 0.7924 (mmm) REVERT: B 335 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7836 (mpm) REVERT: C 106 MET cc_start: 0.8241 (mmt) cc_final: 0.7973 (mmm) REVERT: C 335 MET cc_start: 0.8172 (mmp) cc_final: 0.7859 (mpm) REVERT: D 106 MET cc_start: 0.8248 (mmt) cc_final: 0.7970 (mmm) outliers start: 18 outliers final: 10 residues processed: 148 average time/residue: 1.6021 time to fit residues: 252.4907 Evaluate side-chains 141 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10608 Z= 0.330 Angle : 0.672 9.685 14344 Z= 0.363 Chirality : 0.051 0.184 1592 Planarity : 0.005 0.060 1856 Dihedral : 6.824 58.433 1467 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.32 % Allowed : 18.22 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1360 helix: 0.69 (0.24), residues: 452 sheet: 0.10 (0.27), residues: 332 loop : -0.82 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 PHE 0.014 0.002 PHE A 124 TYR 0.013 0.002 TYR A 311 ARG 0.004 0.001 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.326 Fit side-chains REVERT: A 0 HIS cc_start: 0.6156 (OUTLIER) cc_final: 0.5071 (m-70) REVERT: A 92 THR cc_start: 0.8525 (m) cc_final: 0.8158 (p) REVERT: A 106 MET cc_start: 0.8300 (mmt) cc_final: 0.8021 (mmm) REVERT: A 335 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7970 (mpm) REVERT: B 106 MET cc_start: 0.8235 (mmt) cc_final: 0.7974 (mmm) REVERT: B 335 MET cc_start: 0.8154 (mmp) cc_final: 0.7864 (mpm) REVERT: D 106 MET cc_start: 0.8275 (mmt) cc_final: 0.7981 (mmm) REVERT: D 138 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7703 (ptpp) outliers start: 25 outliers final: 15 residues processed: 149 average time/residue: 1.6330 time to fit residues: 259.4141 Evaluate side-chains 154 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10608 Z= 0.204 Angle : 0.591 9.966 14344 Z= 0.316 Chirality : 0.048 0.222 1592 Planarity : 0.005 0.060 1856 Dihedral : 6.586 58.690 1467 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.04 % Allowed : 18.49 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1360 helix: 0.85 (0.24), residues: 452 sheet: 0.29 (0.28), residues: 328 loop : -0.85 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.004 0.001 HIS C 102 PHE 0.012 0.001 PHE B 124 TYR 0.011 0.002 TYR D 311 ARG 0.002 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.184 Fit side-chains REVERT: A 0 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5025 (m-70) REVERT: A 92 THR cc_start: 0.8430 (m) cc_final: 0.8075 (p) REVERT: A 106 MET cc_start: 0.8203 (mmt) cc_final: 0.7920 (mmm) REVERT: A 335 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7948 (mpm) REVERT: B 106 MET cc_start: 0.8212 (mmt) cc_final: 0.7966 (mmm) REVERT: B 335 MET cc_start: 0.8097 (mmp) cc_final: 0.7847 (mpm) REVERT: C 106 MET cc_start: 0.8262 (mmt) cc_final: 0.8042 (mmm) REVERT: C 138 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7721 (ptpp) REVERT: C 335 MET cc_start: 0.8117 (mmp) cc_final: 0.7847 (mpm) REVERT: D 106 MET cc_start: 0.8228 (mmt) cc_final: 0.7925 (mmm) REVERT: D 335 MET cc_start: 0.8246 (mmp) cc_final: 0.7964 (mpm) outliers start: 22 outliers final: 14 residues processed: 144 average time/residue: 1.6222 time to fit residues: 248.7295 Evaluate side-chains 144 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10608 Z= 0.250 Angle : 0.624 10.030 14344 Z= 0.336 Chirality : 0.049 0.206 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.684 58.500 1467 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.77 % Allowed : 18.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1360 helix: 0.76 (0.24), residues: 452 sheet: 0.21 (0.28), residues: 308 loop : -0.87 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS C 102 PHE 0.013 0.001 PHE A 124 TYR 0.012 0.002 TYR A 311 ARG 0.003 0.000 ARG D 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.344 Fit side-chains REVERT: A 0 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5057 (m-70) REVERT: A 92 THR cc_start: 0.8480 (m) cc_final: 0.8119 (p) REVERT: A 106 MET cc_start: 0.8253 (mmt) cc_final: 0.7970 (mmm) REVERT: A 335 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7951 (mpm) REVERT: B 106 MET cc_start: 0.8226 (mmt) cc_final: 0.7941 (mmm) REVERT: B 335 MET cc_start: 0.8146 (mmp) cc_final: 0.7904 (mpm) REVERT: C 106 MET cc_start: 0.8246 (mmt) cc_final: 0.7953 (mmm) REVERT: C 138 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7727 (ptpp) REVERT: C 335 MET cc_start: 0.8149 (mmp) cc_final: 0.7874 (mpm) REVERT: D 106 MET cc_start: 0.8246 (mmt) cc_final: 0.7955 (mmm) REVERT: D 335 MET cc_start: 0.8231 (mmp) cc_final: 0.7924 (mpm) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 1.5294 time to fit residues: 227.9325 Evaluate side-chains 146 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 0.0070 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111538 restraints weight = 8847.554| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.33 r_work: 0.3181 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10608 Z= 0.143 Angle : 0.540 10.413 14344 Z= 0.286 Chirality : 0.046 0.246 1592 Planarity : 0.004 0.060 1856 Dihedral : 6.204 58.945 1467 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.39 % Allowed : 19.24 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1360 helix: 1.12 (0.25), residues: 452 sheet: 0.58 (0.30), residues: 304 loop : -0.85 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.011 0.001 PHE B 124 TYR 0.009 0.001 TYR D 311 ARG 0.001 0.000 ARG A 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4393.42 seconds wall clock time: 81 minutes 29.25 seconds (4889.25 seconds total)