Starting phenix.real_space_refine on Fri Nov 15 01:07:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti8_41281/11_2024/8ti8_41281.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 16 5.16 5 C 5053 2.51 5 N 1281 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7887 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1901 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain: "C" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2093 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "D" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2052 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1841 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 6.30, per 1000 atoms: 0.80 Number of scatterers: 7887 At special positions: 0 Unit cell: (79.8, 82.32, 146.16, 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 16 16.00 O 1537 8.00 N 1281 7.00 C 5053 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: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 62.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 159 through 169 removed outlier: 4.281A pdb=" N ILE A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 197 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.578A pdb=" N TRP A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.624A pdb=" N PHE A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 318 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.508A pdb=" N ARG A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.643A pdb=" N SER C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.543A pdb=" N ILE C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 198 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.532A pdb=" N TRP C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.937A pdb=" N PHE C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 317 removed outlier: 3.571A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.651A pdb=" N THR C 339 " --> pdb=" O MET C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.525A pdb=" N ARG C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 380 Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 131 through 141 removed outlier: 3.953A pdb=" N LEU D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 159 through 168 removed outlier: 3.839A pdb=" N ILE D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 198 Processing helix chain 'D' and resid 203 through 213 Processing helix chain 'D' and resid 214 through 223 removed outlier: 3.826A pdb=" N LEU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.856A pdb=" N PHE D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 318 removed outlier: 3.556A pdb=" N THR D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 Processing helix chain 'D' and resid 364 through 379 Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 159 through 168 Processing helix chain 'B' and resid 171 through 197 Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.631A pdb=" N TRP B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 removed outlier: 3.798A pdb=" N LEU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.772A pdb=" N PHE B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 316 removed outlier: 3.538A pdb=" N THR B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 Processing helix chain 'B' and resid 363 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.852A pdb=" N LYS A 238 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS A 330 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE A 362 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 332 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'D' and resid 273 through 274 removed outlier: 4.389A pdb=" N SER D 284 " --> pdb=" O THR D 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 238 through 240 removed outlier: 4.760A pdb=" N ALA B 233 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.939A pdb=" N SER B 284 " --> pdb=" O THR B 274 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1419 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: 2.14 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2526 1.34 - 1.46: 1227 1.46 - 1.57: 4248 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 8025 Sorted by residual: bond pdb=" N VAL C 235 " pdb=" CA VAL C 235 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.58e+00 bond pdb=" N LYS D 171 " pdb=" CA LYS D 171 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.37e-02 5.33e+03 7.35e+00 bond pdb=" N LEU D 170 " pdb=" CA LEU D 170 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.32e-02 5.74e+03 7.08e+00 bond pdb=" N LYS C 238 " pdb=" CA LYS C 238 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.73e+00 bond pdb=" N LEU D 167 " pdb=" CA LEU D 167 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.52e+00 ... (remaining 8020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 10147 0.79 - 1.59: 582 1.59 - 2.38: 114 2.38 - 3.18: 35 3.18 - 3.97: 13 Bond angle restraints: 10891 Sorted by residual: angle pdb=" CA LEU D 170 " pdb=" C LEU D 170 " pdb=" O LEU D 170 " ideal model delta sigma weight residual 121.87 117.90 3.97 1.10e+00 8.26e-01 1.30e+01 angle pdb=" CA LYS D 171 " pdb=" C LYS D 171 " pdb=" O LYS D 171 " ideal model delta sigma weight residual 121.99 118.15 3.84 1.14e+00 7.69e-01 1.14e+01 angle pdb=" C GLY A 236 " pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta sigma weight residual 123.30 120.55 2.75 1.06e+00 8.90e-01 6.75e+00 angle pdb=" N GLY C 237 " pdb=" CA GLY C 237 " pdb=" C GLY C 237 " ideal model delta sigma weight residual 115.30 111.69 3.61 1.44e+00 4.82e-01 6.27e+00 angle pdb=" CA LEU D 167 " pdb=" C LEU D 167 " pdb=" O LEU D 167 " ideal model delta sigma weight residual 120.55 117.91 2.64 1.06e+00 8.90e-01 6.18e+00 ... (remaining 10886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 4461 11.70 - 23.40: 322 23.40 - 35.10: 55 35.10 - 46.80: 15 46.80 - 58.51: 8 Dihedral angle restraints: 4861 sinusoidal: 1977 harmonic: 2884 Sorted by residual: dihedral pdb=" CA PHE B 368 " pdb=" C PHE B 368 " pdb=" N GLU B 369 " pdb=" CA GLU B 369 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PHE D 368 " pdb=" C PHE D 368 " pdb=" N GLU D 369 " pdb=" CA GLU D 369 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS B 320 " pdb=" CB LYS B 320 " pdb=" CG LYS B 320 " pdb=" CD LYS B 320 " ideal model delta sinusoidal sigma weight residual 60.00 118.51 -58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 926 0.033 - 0.067: 247 0.067 - 0.100: 92 0.100 - 0.134: 31 0.134 - 0.167: 3 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA VAL C 235 " pdb=" N VAL C 235 " pdb=" C VAL C 235 " pdb=" CB VAL C 235 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA LEU D 170 " pdb=" N LEU D 170 " pdb=" C LEU D 170 " pdb=" CB LEU D 170 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA PHE A 368 " pdb=" N PHE A 368 " pdb=" C PHE A 368 " pdb=" CB PHE A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1296 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 254 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO C 255 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 254 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO D 255 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 254 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO B 255 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.017 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1807 2.80 - 3.33: 7455 3.33 - 3.85: 12300 3.85 - 4.38: 14113 4.38 - 4.90: 24776 Nonbonded interactions: 60451 Sorted by model distance: nonbonded pdb=" ND2 ASN A 254 " pdb=" O SER A 257 " model vdw 2.277 3.120 nonbonded pdb=" OE1 GLU A 232 " pdb=" OH TYR A 234 " model vdw 2.315 3.040 nonbonded pdb=" NZ LYS A 354 " pdb=" OD1 ASP B 324 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN C 254 " pdb=" O SER C 257 " model vdw 2.365 3.120 nonbonded pdb=" O PHE C 256 " pdb=" NH1 ARG D 370 " model vdw 2.386 3.120 ... (remaining 60446 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' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 275 or resid 282 through 379)) \ selection = (chain 'B' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 379)) selection = (chain 'C' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 275 or resid 282 through 379)) \ selection = (chain 'D' and resid 147 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.340 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 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 : 0.003 0.037 8025 Z= 0.183 Angle : 0.461 3.971 10891 Z= 0.298 Chirality : 0.039 0.167 1299 Planarity : 0.003 0.037 1363 Dihedral : 8.827 58.505 2981 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.66 % Allowed : 1.88 % Favored : 97.46 % 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: 2.48 (0.29), residues: 964 helix: 2.81 (0.21), residues: 610 sheet: 2.37 (0.89), residues: 54 loop : -1.12 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 207 HIS 0.002 0.000 HIS A 347 PHE 0.016 0.001 PHE B 368 TYR 0.007 0.001 TYR D 307 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8367 (m-30) cc_final: 0.8089 (p0) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 1.5964 time to fit residues: 162.2987 Evaluate side-chains 45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain D residue 231 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 86 optimal weight: 0.0470 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 177 GLN D 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8025 Z= 0.142 Angle : 0.429 7.505 10891 Z= 0.226 Chirality : 0.039 0.135 1299 Planarity : 0.003 0.033 1363 Dihedral : 3.385 14.755 1034 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.11 % Allowed : 6.53 % Favored : 92.37 % 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: 2.48 (0.29), residues: 964 helix: 2.75 (0.21), residues: 621 sheet: 1.69 (0.87), residues: 56 loop : -0.96 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 207 HIS 0.001 0.001 HIS C 286 PHE 0.014 0.001 PHE B 368 TYR 0.013 0.001 TYR C 315 ARG 0.007 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.7061 (m110) REVERT: A 316 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8044 (mtt90) REVERT: A 322 ASP cc_start: 0.8381 (m-30) cc_final: 0.8040 (p0) REVERT: D 134 LEU cc_start: 0.8848 (mt) cc_final: 0.8561 (tt) REVERT: D 144 SER cc_start: 0.8923 (t) cc_final: 0.8621 (p) REVERT: B 347 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (t70) outliers start: 10 outliers final: 0 residues processed: 59 average time/residue: 1.3334 time to fit residues: 83.8080 Evaluate side-chains 45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8025 Z= 0.189 Angle : 0.419 7.183 10891 Z= 0.226 Chirality : 0.039 0.136 1299 Planarity : 0.003 0.029 1363 Dihedral : 3.365 14.470 1030 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.00 % Allowed : 7.74 % Favored : 91.26 % 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: 2.44 (0.28), residues: 964 helix: 2.72 (0.21), residues: 622 sheet: 1.46 (0.85), residues: 56 loop : -0.96 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 207 HIS 0.002 0.000 HIS C 347 PHE 0.016 0.001 PHE B 368 TYR 0.010 0.001 TYR B 307 ARG 0.006 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7079 (m110) REVERT: A 316 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8048 (mtt90) REVERT: A 322 ASP cc_start: 0.8394 (m-30) cc_final: 0.8031 (p0) REVERT: D 134 LEU cc_start: 0.8874 (mt) cc_final: 0.8565 (tt) outliers start: 9 outliers final: 2 residues processed: 49 average time/residue: 1.2520 time to fit residues: 65.9921 Evaluate side-chains 44 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain B residue 267 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8025 Z= 0.311 Angle : 0.474 7.662 10891 Z= 0.257 Chirality : 0.041 0.152 1299 Planarity : 0.003 0.035 1363 Dihedral : 3.578 16.662 1030 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.00 % Allowed : 8.30 % Favored : 90.71 % 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: 2.20 (0.28), residues: 964 helix: 2.55 (0.21), residues: 620 sheet: 1.16 (0.82), residues: 56 loop : -1.02 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 207 HIS 0.002 0.001 HIS A 347 PHE 0.019 0.002 PHE D 368 TYR 0.015 0.001 TYR B 307 ARG 0.004 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8404 (m-30) cc_final: 0.8041 (p0) REVERT: D 134 LEU cc_start: 0.8921 (mt) cc_final: 0.8591 (tt) REVERT: B 347 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8019 (t70) outliers start: 9 outliers final: 2 residues processed: 47 average time/residue: 1.2829 time to fit residues: 64.8238 Evaluate side-chains 42 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8025 Z= 0.173 Angle : 0.415 8.399 10891 Z= 0.224 Chirality : 0.039 0.133 1299 Planarity : 0.003 0.032 1363 Dihedral : 3.437 14.749 1030 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.88 % Allowed : 8.41 % Favored : 90.71 % 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: 2.34 (0.28), residues: 964 helix: 2.65 (0.21), residues: 622 sheet: 1.19 (0.82), residues: 56 loop : -0.96 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 286 PHE 0.016 0.001 PHE C 368 TYR 0.019 0.001 TYR C 315 ARG 0.007 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8068 (mtt90) REVERT: A 322 ASP cc_start: 0.8394 (m-30) cc_final: 0.7998 (p0) REVERT: D 134 LEU cc_start: 0.8876 (mt) cc_final: 0.8548 (tt) REVERT: B 347 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.8028 (t70) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 1.2344 time to fit residues: 62.5021 Evaluate side-chains 44 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8025 Z= 0.206 Angle : 0.434 8.671 10891 Z= 0.232 Chirality : 0.039 0.137 1299 Planarity : 0.003 0.033 1363 Dihedral : 3.420 14.722 1030 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.55 % Allowed : 8.96 % Favored : 90.49 % 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: 2.31 (0.28), residues: 964 helix: 2.62 (0.21), residues: 622 sheet: 1.14 (0.81), residues: 56 loop : -0.95 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 286 PHE 0.016 0.001 PHE C 368 TYR 0.011 0.001 TYR B 307 ARG 0.007 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8413 (m-30) cc_final: 0.8033 (p0) REVERT: D 134 LEU cc_start: 0.8876 (mt) cc_final: 0.8549 (tt) REVERT: B 347 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.8025 (t70) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 1.1511 time to fit residues: 60.8807 Evaluate side-chains 46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8025 Z= 0.174 Angle : 0.421 8.773 10891 Z= 0.224 Chirality : 0.039 0.132 1299 Planarity : 0.003 0.032 1363 Dihedral : 3.368 14.687 1030 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.77 % Allowed : 9.07 % Favored : 90.15 % 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: 2.41 (0.28), residues: 964 helix: 2.70 (0.21), residues: 621 sheet: 1.22 (0.81), residues: 56 loop : -0.91 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 207 HIS 0.002 0.000 HIS B 286 PHE 0.016 0.001 PHE C 368 TYR 0.011 0.001 TYR D 283 ARG 0.006 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8398 (m-30) cc_final: 0.7972 (p0) REVERT: D 134 LEU cc_start: 0.8858 (mt) cc_final: 0.8525 (tt) REVERT: B 347 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.8039 (t70) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 1.3018 time to fit residues: 66.8669 Evaluate side-chains 46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8025 Z= 0.194 Angle : 0.429 8.254 10891 Z= 0.229 Chirality : 0.039 0.135 1299 Planarity : 0.003 0.032 1363 Dihedral : 3.374 14.730 1030 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.77 % Allowed : 9.51 % Favored : 89.71 % 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: 2.41 (0.28), residues: 964 helix: 2.70 (0.21), residues: 620 sheet: 1.23 (0.81), residues: 56 loop : -0.89 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 286 PHE 0.016 0.001 PHE C 368 TYR 0.011 0.001 TYR B 283 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8406 (m-30) cc_final: 0.7979 (p0) REVERT: D 134 LEU cc_start: 0.8851 (mt) cc_final: 0.8518 (tt) REVERT: B 316 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7828 (tpt90) REVERT: B 347 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.8040 (t70) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 1.3228 time to fit residues: 66.6795 Evaluate side-chains 46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8025 Z= 0.148 Angle : 0.406 8.749 10891 Z= 0.216 Chirality : 0.038 0.130 1299 Planarity : 0.003 0.031 1363 Dihedral : 3.285 14.532 1030 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.77 % Allowed : 9.51 % Favored : 89.71 % 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: 2.58 (0.29), residues: 964 helix: 2.84 (0.21), residues: 619 sheet: 1.28 (0.82), residues: 56 loop : -0.82 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 207 HIS 0.001 0.000 HIS B 286 PHE 0.016 0.001 PHE C 368 TYR 0.011 0.001 TYR D 283 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8392 (m-30) cc_final: 0.7960 (p0) REVERT: D 134 LEU cc_start: 0.8871 (mt) cc_final: 0.8576 (tt) REVERT: B 316 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7780 (tpt90) REVERT: B 347 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.8021 (t70) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 1.2903 time to fit residues: 66.7215 Evaluate side-chains 46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8025 Z= 0.154 Angle : 0.432 10.765 10891 Z= 0.226 Chirality : 0.039 0.188 1299 Planarity : 0.003 0.031 1363 Dihedral : 3.264 14.519 1030 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.55 % Allowed : 9.96 % Favored : 89.49 % 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: 2.64 (0.29), residues: 964 helix: 2.88 (0.21), residues: 618 sheet: 1.28 (0.81), residues: 56 loop : -0.77 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 207 HIS 0.001 0.000 HIS A 347 PHE 0.015 0.001 PHE C 368 TYR 0.012 0.001 TYR D 283 ARG 0.005 0.000 ARG B 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8385 (m-30) cc_final: 0.7946 (p0) REVERT: D 134 LEU cc_start: 0.8869 (mt) cc_final: 0.8585 (tt) REVERT: B 316 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7755 (tpt90) REVERT: B 347 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (t70) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 1.3058 time to fit residues: 64.4577 Evaluate side-chains 45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060419 restraints weight = 15421.710| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.86 r_work: 0.2721 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8025 Z= 0.326 Angle : 0.507 12.876 10891 Z= 0.267 Chirality : 0.041 0.155 1299 Planarity : 0.003 0.036 1363 Dihedral : 3.534 15.834 1030 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.44 % Allowed : 10.07 % Favored : 89.49 % 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: 2.32 (0.28), residues: 964 helix: 2.65 (0.21), residues: 616 sheet: 1.10 (0.79), residues: 56 loop : -0.91 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 194 HIS 0.002 0.001 HIS B 286 PHE 0.020 0.002 PHE D 368 TYR 0.022 0.001 TYR C 315 ARG 0.005 0.000 ARG B 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.11 seconds wall clock time: 43 minutes 18.91 seconds (2598.91 seconds total)