Starting phenix.real_space_refine on Sun Mar 10 15:46:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/03_2024/6x13_21987_updated.pdb" } resolution = 3.66 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= 0.003 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 P 1 5.49 5 S 18 5.16 5 C 2067 2.51 5 N 501 2.21 5 O 549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3136 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3136 Unusual residues: {'6OU': 1} Classifications: {'peptide': 417, 'undetermined': 1} Link IDs: {'PTRANS': 18, 'TRANS': 398, None: 1} Not linked: pdbres="THR A 418 " pdbres="6OU A 501 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.32, per 1000 atoms: 0.74 Number of scatterers: 3136 At special positions: 0 Unit cell: (66.5415, 78.3473, 71.9078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 549 8.00 N 501 7.00 C 2067 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: 1.26 Conformation dependent library (CDL) restraints added in 617.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 37 through 71 removed outlier: 3.767A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.340A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.929A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 106 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.213A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 219 removed outlier: 3.850A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.771A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 296 through 308 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 377 through 417 removed outlier: 3.754A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 687 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: 0.74 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 482 1.31 - 1.43: 788 1.43 - 1.56: 1878 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3196 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.562 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.580 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.67: 95 106.67 - 113.29: 1814 113.29 - 119.91: 1066 119.91 - 126.53: 1344 126.53 - 133.15: 30 Bond angle restraints: 4349 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.38 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.46 -10.65 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.34e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C THR A 275 " pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 122.08 127.30 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 1768 25.76 - 51.51: 101 51.51 - 77.27: 16 77.27 - 103.03: 2 103.03 - 128.78: 2 Dihedral angle restraints: 1889 sinusoidal: 707 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LEU A 372 " pdb=" C LEU A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C09 6OU A 501 " pdb=" C10 6OU A 501 " pdb=" C11 6OU A 501 " pdb=" C12 6OU A 501 " ideal model delta sinusoidal sigma weight residual 179.71 -51.51 -128.78 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C20 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " pdb=" C33 6OU A 501 " ideal model delta sinusoidal sigma weight residual -177.41 -63.97 -113.44 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 1886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 347 0.040 - 0.080: 138 0.080 - 0.119: 43 0.119 - 0.159: 7 0.159 - 0.199: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 537 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 45 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 303 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 304 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.031 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1024 2.85 - 3.36: 3094 3.36 - 3.88: 5142 3.88 - 4.39: 5510 4.39 - 4.90: 9835 Nonbonded interactions: 24605 Sorted by model distance: nonbonded pdb=" O LYS A 414 " pdb=" OG1 THR A 418 " model vdw 2.340 2.440 nonbonded pdb=" OD1 ASP A 390 " pdb=" NH1 ARG A 397 " model vdw 2.402 2.520 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.438 2.440 nonbonded pdb=" NZ LYS A 196 " pdb=" O24 6OU A 501 " model vdw 2.439 2.520 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 177 " model vdw 2.454 2.520 ... (remaining 24600 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.410 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.007 0.086 3196 Z= 0.413 Angle : 1.044 15.434 4349 Z= 0.516 Chirality : 0.048 0.199 540 Planarity : 0.008 0.065 533 Dihedral : 16.899 128.781 1141 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.27 % 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: -3.73 (0.31), residues: 415 helix: -2.04 (0.20), residues: 351 sheet: None (None), residues: 0 loop : -3.62 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 264 PHE 0.009 0.001 PHE A 210 TYR 0.017 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.344 Fit side-chains REVERT: A 35 TYR cc_start: 0.7029 (m-80) cc_final: 0.6827 (m-10) REVERT: A 59 MET cc_start: 0.9460 (tpp) cc_final: 0.9200 (mmm) REVERT: A 202 MET cc_start: 0.8192 (mmm) cc_final: 0.7863 (mmm) REVERT: A 362 MET cc_start: 0.7455 (ttm) cc_final: 0.7149 (ttm) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1638 time to fit residues: 12.1494 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3196 Z= 0.181 Angle : 0.583 6.675 4349 Z= 0.299 Chirality : 0.038 0.119 540 Planarity : 0.006 0.069 533 Dihedral : 10.872 90.768 481 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.23 % Allowed : 13.54 % Favored : 85.23 % 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: -0.77 (0.39), residues: 415 helix: 0.16 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -3.73 (0.58), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.005 0.001 PHE A 273 TYR 0.032 0.001 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.337 Fit side-chains REVERT: A 103 MET cc_start: 0.8431 (mmm) cc_final: 0.7930 (tpt) REVERT: A 169 MET cc_start: 0.8552 (tpp) cc_final: 0.7899 (ttm) REVERT: A 362 MET cc_start: 0.7381 (ttm) cc_final: 0.6963 (ttm) REVERT: A 374 LEU cc_start: 0.8766 (tp) cc_final: 0.8470 (tp) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 0.1248 time to fit residues: 9.4631 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3196 Z= 0.198 Angle : 0.581 6.420 4349 Z= 0.298 Chirality : 0.038 0.123 540 Planarity : 0.005 0.073 533 Dihedral : 9.253 91.932 481 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.54 % Allowed : 16.31 % Favored : 82.15 % 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: 0.21 (0.42), residues: 415 helix: 0.86 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -3.65 (0.59), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.008 0.001 PHE A 273 TYR 0.027 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.329 Fit side-chains REVERT: A 103 MET cc_start: 0.8414 (mmm) cc_final: 0.8176 (tpt) REVERT: A 169 MET cc_start: 0.8449 (tpp) cc_final: 0.7917 (ttm) REVERT: A 362 MET cc_start: 0.7475 (ttm) cc_final: 0.7060 (ttm) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1395 time to fit residues: 10.4274 Evaluate side-chains 53 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3196 Z= 0.188 Angle : 0.569 6.297 4349 Z= 0.291 Chirality : 0.038 0.136 540 Planarity : 0.005 0.074 533 Dihedral : 8.110 78.717 481 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % 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: 0.77 (0.43), residues: 415 helix: 1.24 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.38 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.007 0.001 PHE A 273 TYR 0.025 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.403 Fit side-chains REVERT: A 103 MET cc_start: 0.8401 (mmm) cc_final: 0.8145 (tpt) REVERT: A 169 MET cc_start: 0.8447 (tpp) cc_final: 0.7919 (ttm) REVERT: A 362 MET cc_start: 0.7558 (ttm) cc_final: 0.7078 (ttm) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1402 time to fit residues: 10.4992 Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3196 Z= 0.207 Angle : 0.579 6.281 4349 Z= 0.297 Chirality : 0.039 0.189 540 Planarity : 0.005 0.077 533 Dihedral : 7.689 77.659 481 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.46 % Allowed : 19.69 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.42), residues: 415 helix: 1.36 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.27 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.008 0.001 PHE A 273 TYR 0.023 0.002 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.347 Fit side-chains REVERT: A 169 MET cc_start: 0.8468 (tpp) cc_final: 0.7946 (ttm) REVERT: A 362 MET cc_start: 0.7613 (ttm) cc_final: 0.7113 (ttm) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1358 time to fit residues: 10.7182 Evaluate side-chains 53 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3196 Z= 0.234 Angle : 0.603 8.452 4349 Z= 0.307 Chirality : 0.039 0.144 540 Planarity : 0.005 0.080 533 Dihedral : 7.632 78.607 481 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.08 % Allowed : 20.62 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.42), residues: 415 helix: 1.38 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -3.11 (0.63), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.009 0.001 PHE A 273 TYR 0.022 0.002 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.352 Fit side-chains REVERT: A 169 MET cc_start: 0.8527 (tpp) cc_final: 0.8004 (ttm) REVERT: A 362 MET cc_start: 0.7631 (ttm) cc_final: 0.7134 (ttm) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1435 time to fit residues: 10.1928 Evaluate side-chains 53 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0040 chunk 25 optimal weight: 0.0970 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3196 Z= 0.174 Angle : 0.578 8.114 4349 Z= 0.293 Chirality : 0.039 0.177 540 Planarity : 0.005 0.081 533 Dihedral : 7.309 73.500 481 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 21.85 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.43), residues: 415 helix: 1.57 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -2.94 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 261 TYR 0.022 0.002 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.329 Fit side-chains REVERT: A 169 MET cc_start: 0.8489 (tpp) cc_final: 0.7995 (ttm) REVERT: A 362 MET cc_start: 0.7595 (ttm) cc_final: 0.7103 (ttm) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1492 time to fit residues: 11.0220 Evaluate side-chains 56 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3196 Z= 0.206 Angle : 0.626 12.168 4349 Z= 0.309 Chirality : 0.039 0.167 540 Planarity : 0.005 0.083 533 Dihedral : 7.252 72.760 481 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.15 % Allowed : 23.08 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.43), residues: 415 helix: 1.58 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -2.83 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.007 0.001 PHE A 261 TYR 0.022 0.002 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.355 Fit side-chains REVERT: A 169 MET cc_start: 0.8459 (tpp) cc_final: 0.7985 (ttm) REVERT: A 362 MET cc_start: 0.7613 (ttm) cc_final: 0.7105 (ttm) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.1413 time to fit residues: 10.8570 Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3196 Z= 0.259 Angle : 0.650 11.046 4349 Z= 0.323 Chirality : 0.040 0.166 540 Planarity : 0.005 0.084 533 Dihedral : 7.418 74.679 481 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.54 % Allowed : 23.38 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.43), residues: 415 helix: 1.57 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -2.58 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 40 PHE 0.006 0.001 PHE A 261 TYR 0.025 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.341 Fit side-chains REVERT: A 169 MET cc_start: 0.8485 (tpp) cc_final: 0.7996 (ttm) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1432 time to fit residues: 9.6076 Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3196 Z= 0.221 Angle : 0.640 10.965 4349 Z= 0.317 Chirality : 0.039 0.176 540 Planarity : 0.005 0.084 533 Dihedral : 7.328 72.517 481 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.54 % Allowed : 23.08 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.43), residues: 415 helix: 1.57 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -2.33 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.007 0.001 PHE A 261 TYR 0.025 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.338 Fit side-chains REVERT: A 169 MET cc_start: 0.8474 (tpp) cc_final: 0.8009 (ttm) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1441 time to fit residues: 9.8519 Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 401 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098377 restraints weight = 4265.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100794 restraints weight = 2920.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102505 restraints weight = 2269.544| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3196 Z= 0.217 Angle : 0.638 11.116 4349 Z= 0.316 Chirality : 0.039 0.178 540 Planarity : 0.005 0.081 533 Dihedral : 7.273 71.177 481 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.54 % Allowed : 22.77 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.43), residues: 415 helix: 1.63 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.87 (0.77), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.007 0.001 PHE A 261 TYR 0.025 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.68 seconds wall clock time: 19 minutes 12.25 seconds (1152.25 seconds total)