Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 13:54:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/08_2023/8f6t_28890_updated.pdb" } resolution = 2.76 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= 0.008 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 11 5.16 5 C 2261 2.51 5 N 604 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 3473 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3473 Unusual residues: {' FE': 3, 'D12': 1} Classifications: {'peptide': 428, 'undetermined': 4} Link IDs: {'PTRANS': 30, 'TRANS': 397, None: 4} Not linked: pdbres="ALA A 467 " pdbres=" FE A 501 " Not linked: pdbres=" FE A 501 " pdbres=" FE A 502 " Not linked: pdbres=" FE A 502 " pdbres=" FE A 503 " Not linked: pdbres=" FE A 503 " pdbres="D12 A 504 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 418 40.499 23.954 46.620 1.00125.12 S ATOM 3095 SG CYS A 421 40.898 27.411 46.825 1.00127.79 S ATOM 3331 SG CYS A 451 38.727 26.710 49.011 1.00124.73 S ATOM 3352 SG CYS A 454 37.613 26.470 45.458 1.00120.95 S Time building chain proxies: 2.32, per 1000 atoms: 0.67 Number of scatterers: 3473 At special positions: 0 Unit cell: (65.268, 81.252, 75.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 3 26.01 S 11 16.00 O 594 8.00 N 604 7.00 C 2261 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: 1.63 Conformation dependent library (CDL) restraints added in 706.9 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 0 sheets defined 56.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.613A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Proline residue: A 25 - end of helix Proline residue: A 28 - end of helix removed outlier: 4.106A pdb=" N THR A 41 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 58 through 64 removed outlier: 4.890A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 4.258A pdb=" N ALA A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 110 removed outlier: 4.041A pdb=" N VAL A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix removed outlier: 3.854A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.664A pdb=" N TRP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.773A pdb=" N HIS A 167 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 194 through 215 Processing helix chain 'A' and resid 226 through 244 removed outlier: 3.910A pdb=" N MET A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 348 through 362 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 374 through 384 removed outlier: 5.467A pdb=" N ALA A 378 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP A 384 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' 129 hydrogen bonds defined for protein. 318 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: 0.82 Time building geometry restraints manager: 1.52 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: 1104 1.34 - 1.46: 717 1.46 - 1.57: 1749 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 3585 Sorted by residual: bond pdb=" CA HIS A 314 " pdb=" C HIS A 314 " ideal model delta sigma weight residual 1.523 1.512 0.011 1.30e-02 5.92e+03 7.03e-01 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.39e-01 bond pdb=" CG1 ILE A 131 " pdb=" CD1 ILE A 131 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.31e-01 bond pdb=" N GLU A 271 " pdb=" CA GLU A 271 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.19e-02 7.06e+03 5.20e-01 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 5.02e-01 ... (remaining 3580 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 151 106.60 - 113.45: 1905 113.45 - 120.30: 1391 120.30 - 127.15: 1375 127.15 - 134.00: 76 Bond angle restraints: 4898 Sorted by residual: angle pdb=" N ASP A 453 " pdb=" CA ASP A 453 " pdb=" C ASP A 453 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" N CYS A 454 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.09e+00 angle pdb=" C ASN A 168 " pdb=" N ARG A 169 " pdb=" CA ARG A 169 " ideal model delta sigma weight residual 121.99 118.70 3.29 1.56e+00 4.11e-01 4.46e+00 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" O ASP A 453 " ideal model delta sigma weight residual 118.55 120.78 -2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" N PRO A 374 " pdb=" CA PRO A 374 " pdb=" C PRO A 374 " ideal model delta sigma weight residual 110.70 112.87 -2.17 1.22e+00 6.72e-01 3.17e+00 ... (remaining 4893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1849 16.14 - 32.29: 184 32.29 - 48.43: 38 48.43 - 64.57: 2 64.57 - 80.71: 1 Dihedral angle restraints: 2074 sinusoidal: 830 harmonic: 1244 Sorted by residual: dihedral pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta harmonic sigma weight residual 180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 267 0.027 - 0.053: 151 0.053 - 0.080: 64 0.080 - 0.107: 27 0.107 - 0.134: 7 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG A 169 " pdb=" N ARG A 169 " pdb=" C ARG A 169 " pdb=" CB ARG A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 513 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 373 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 374 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 180 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 181 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 440 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 441 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.019 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 52 2.68 - 3.23: 3390 3.23 - 3.79: 5331 3.79 - 4.34: 7214 4.34 - 4.90: 11797 Nonbonded interactions: 27784 Sorted by model distance: nonbonded pdb=" NE2 HIS A 167 " pdb="FE FE A 502 " model vdw 2.119 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 501 " model vdw 2.163 2.340 nonbonded pdb=" NE2 HIS A 314 " pdb="FE FE A 502 " model vdw 2.167 2.340 nonbonded pdb=" NE2 HIS A 141 " pdb="FE FE A 502 " model vdw 2.198 2.340 nonbonded pdb=" ND2 ASN A 129 " pdb=" OE1 GLN A 256 " model vdw 2.215 2.520 ... (remaining 27779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.800 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.004 0.029 3585 Z= 0.281 Angle : 0.629 6.030 4898 Z= 0.344 Chirality : 0.041 0.134 516 Planarity : 0.005 0.049 624 Dihedral : 12.871 80.711 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.00 % 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: 0.80 (0.42), residues: 424 helix: 1.16 (0.36), residues: 239 sheet: None (None), residues: 0 loop : -0.22 (0.45), residues: 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.471 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.0822 time to fit residues: 33.9855 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3585 Z= 0.172 Angle : 0.540 7.495 4898 Z= 0.268 Chirality : 0.038 0.129 516 Planarity : 0.005 0.046 624 Dihedral : 5.352 49.923 485 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.42), residues: 424 helix: 1.11 (0.36), residues: 233 sheet: None (None), residues: 0 loop : -0.29 (0.45), residues: 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.420 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 0.9640 time to fit residues: 24.4595 Evaluate side-chains 20 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0377 time to fit residues: 0.5965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3585 Z= 0.155 Angle : 0.501 5.831 4898 Z= 0.250 Chirality : 0.037 0.129 516 Planarity : 0.005 0.044 624 Dihedral : 5.045 48.406 485 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.42), residues: 424 helix: 1.09 (0.36), residues: 232 sheet: None (None), residues: 0 loop : -0.18 (0.46), residues: 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.396 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.9210 time to fit residues: 28.2024 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0747 time to fit residues: 0.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3585 Z= 0.184 Angle : 0.515 5.756 4898 Z= 0.255 Chirality : 0.037 0.127 516 Planarity : 0.005 0.044 624 Dihedral : 5.056 52.136 485 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.42), residues: 424 helix: 1.10 (0.36), residues: 232 sheet: 0.55 (1.85), residues: 9 loop : -0.41 (0.47), residues: 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.422 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.9539 time to fit residues: 28.2113 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0789 time to fit residues: 0.6484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3585 Z= 0.189 Angle : 0.517 5.706 4898 Z= 0.254 Chirality : 0.038 0.127 516 Planarity : 0.005 0.044 624 Dihedral : 5.082 54.678 485 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.40 % 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: 0.70 (0.42), residues: 424 helix: 1.07 (0.36), residues: 231 sheet: None (None), residues: 0 loop : -0.17 (0.46), residues: 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.407 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 1.0569 time to fit residues: 28.8541 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0777 time to fit residues: 0.6387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 3585 Z= 0.162 Angle : 0.505 5.685 4898 Z= 0.252 Chirality : 0.037 0.128 516 Planarity : 0.005 0.044 624 Dihedral : 4.974 54.425 485 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.40 % 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: 0.57 (0.42), residues: 424 helix: 1.02 (0.36), residues: 231 sheet: 0.59 (1.86), residues: 9 loop : -0.37 (0.47), residues: 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.405 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 28 average time/residue: 1.0400 time to fit residues: 30.5695 Evaluate side-chains 26 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0744 time to fit residues: 0.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 3585 Z= 0.238 Angle : 0.550 6.686 4898 Z= 0.273 Chirality : 0.039 0.125 516 Planarity : 0.005 0.044 624 Dihedral : 5.143 58.010 485 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.84 % 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: 0.53 (0.42), residues: 424 helix: 1.00 (0.36), residues: 231 sheet: 0.61 (1.88), residues: 9 loop : -0.41 (0.46), residues: 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.417 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 1.0928 time to fit residues: 27.5667 Evaluate side-chains 24 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0920 time to fit residues: 0.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3585 Z= 0.200 Angle : 0.535 5.671 4898 Z= 0.267 Chirality : 0.038 0.126 516 Planarity : 0.005 0.045 624 Dihedral : 5.044 55.981 485 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.84 % 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: 0.54 (0.42), residues: 424 helix: 0.99 (0.36), residues: 231 sheet: 0.60 (1.85), residues: 9 loop : -0.37 (0.47), residues: 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.382 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 1.0981 time to fit residues: 26.5183 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0806 time to fit residues: 0.6420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3585 Z= 0.270 Angle : 0.557 5.639 4898 Z= 0.280 Chirality : 0.039 0.127 516 Planarity : 0.005 0.045 624 Dihedral : 5.195 56.861 485 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.42), residues: 424 helix: 0.91 (0.37), residues: 231 sheet: 0.57 (1.87), residues: 9 loop : -0.28 (0.46), residues: 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.407 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 1.0037 time to fit residues: 26.4292 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0564 time to fit residues: 0.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.0060 chunk 3 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 0.0010 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3585 Z= 0.184 Angle : 0.547 6.887 4898 Z= 0.274 Chirality : 0.037 0.129 516 Planarity : 0.005 0.045 624 Dihedral : 5.004 54.369 485 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.28 % 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: 0.55 (0.42), residues: 424 helix: 1.04 (0.37), residues: 225 sheet: 0.70 (1.84), residues: 9 loop : -0.39 (0.47), residues: 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.414 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 1.0596 time to fit residues: 26.7915 Evaluate side-chains 23 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 1 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.0020 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 overall best weight: 0.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.069639 restraints weight = 6924.330| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.65 r_work: 0.2800 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 3585 Z= 0.174 Angle : 0.517 5.682 4898 Z= 0.259 Chirality : 0.037 0.128 516 Planarity : 0.005 0.045 624 Dihedral : 4.684 52.911 485 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.28 % 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: 0.62 (0.43), residues: 424 helix: 1.09 (0.37), residues: 225 sheet: 0.73 (1.84), residues: 9 loop : -0.34 (0.46), residues: 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.81 seconds wall clock time: 25 minutes 0.42 seconds (1500.42 seconds total)