Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.pdb" } resolution = 3.1 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } 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= 0.020 sd= 0.076 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 S 9 5.16 5 C 1662 2.51 5 N 380 2.21 5 O 402 1.98 5 H 2490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4943 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4943 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.90, per 1000 atoms: 0.18 Number of scatterers: 4943 At special positions: 0 Unit cell: (56.6, 55.468, 63.392, 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 9 16.00 O 402 8.00 N 380 7.00 C 1662 6.00 H 2490 1.00 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: 1.12 Conformation dependent library (CDL) restraints added in 146.7 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Proline residue: A 17 - end of helix removed outlier: 4.094A pdb=" N LEU A 20 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 22 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 65 removed outlier: 3.774A pdb=" N MET A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 79 through 99 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 102 through 123 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 146 Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 163 through 190 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 195 through 218 removed outlier: 4.734A pdb=" N ALA A 199 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.931A pdb=" N VAL A 210 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 248 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 255 through 276 removed outlier: 4.001A pdb=" N PHE A 262 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 270 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 182 hydrogen bonds defined for protein. 360 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: 0.88 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2489 1.14 - 1.31: 356 1.31 - 1.47: 1106 1.47 - 1.64: 1056 1.64 - 1.80: 17 Bond restraints: 5024 Sorted by residual: bond pdb=" N VAL A 47 " pdb=" H VAL A 47 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N ILE A 46 " pdb=" H ILE A 46 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLY A 263 " pdb=" H GLY A 263 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N ALA A 48 " pdb=" H ALA A 48 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" N SER A 41 " pdb=" H SER A 41 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 5019 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 194 107.32 - 113.99: 5685 113.99 - 120.65: 1992 120.65 - 127.32: 1173 127.32 - 133.98: 38 Bond angle restraints: 9082 Sorted by residual: angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" C PRO A 8 " ideal model delta sigma weight residual 114.20 116.31 -2.11 1.20e+00 6.94e-01 3.10e+00 angle pdb=" CA GLU A 68 " pdb=" CB GLU A 68 " pdb=" CG GLU A 68 " ideal model delta sigma weight residual 114.10 117.03 -2.93 2.00e+00 2.50e-01 2.15e+00 angle pdb=" C ASP A 224 " pdb=" CA ASP A 224 " pdb=" CB ASP A 224 " ideal model delta sigma weight residual 114.11 110.70 3.41 2.44e+00 1.68e-01 1.96e+00 angle pdb=" CA LEU A 9 " pdb=" CB LEU A 9 " pdb=" HB2 LEU A 9 " ideal model delta sigma weight residual 109.00 104.86 4.14 3.00e+00 1.11e-01 1.91e+00 angle pdb=" CG LEU A 9 " pdb=" CB LEU A 9 " pdb=" HB2 LEU A 9 " ideal model delta sigma weight residual 108.00 104.36 3.64 3.00e+00 1.11e-01 1.47e+00 ... (remaining 9077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 2189 16.33 - 32.65: 113 32.65 - 48.98: 50 48.98 - 65.30: 24 65.30 - 81.63: 2 Dihedral angle restraints: 2378 sinusoidal: 1211 harmonic: 1167 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 125.69 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB LYS A 251 " pdb=" CG LYS A 251 " pdb=" CD LYS A 251 " pdb=" CE LYS A 251 " ideal model delta sinusoidal sigma weight residual 180.00 127.03 52.97 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -107.94 47.94 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 2375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 233 0.024 - 0.048: 97 0.048 - 0.072: 33 0.072 - 0.096: 20 0.096 - 0.120: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA VAL A 223 " pdb=" N VAL A 223 " pdb=" C VAL A 223 " pdb=" CB VAL A 223 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 9 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 10 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 7 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 144 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.66e-01 pdb=" N PRO A 145 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.014 5.00e-02 4.00e+02 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 200 2.08 - 2.71: 7346 2.71 - 3.34: 15437 3.34 - 3.97: 20021 3.97 - 4.60: 29916 Nonbonded interactions: 72920 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.447 1.850 nonbonded pdb=" O SER A 261 " pdb=" H ALA A 265 " model vdw 1.487 1.850 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.518 1.850 nonbonded pdb=" O VAL A 212 " pdb=" H LEU A 216 " model vdw 1.531 1.850 nonbonded pdb=" O THR A 121 " pdb=" HG SER A 125 " model vdw 1.553 1.850 ... (remaining 72915 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.030 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: 0.030 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.810 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2534 Z= 0.117 Angle : 0.423 4.250 3457 Z= 0.230 Chirality : 0.036 0.120 390 Planarity : 0.004 0.029 420 Dihedral : 11.751 81.625 856 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.50), residues: 306 helix: 0.10 (0.34), residues: 239 sheet: None (None), residues: 0 loop : 0.53 (0.89), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.006 0.001 TYR A 233 PHE 0.010 0.001 PHE A 197 TRP 0.007 0.001 TRP A 231 HIS 0.001 0.000 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1369 time to fit residues: 4.3117 Evaluate side-chains 24 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2534 Z= 0.219 Angle : 0.439 4.380 3457 Z= 0.233 Chirality : 0.037 0.113 390 Planarity : 0.004 0.028 420 Dihedral : 3.626 21.983 331 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % 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: 1.06 (0.51), residues: 306 helix: 0.86 (0.36), residues: 237 sheet: None (None), residues: 0 loop : 0.56 (0.83), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.006 0.001 TYR A 233 PHE 0.008 0.001 PHE A 133 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.212 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.2900 time to fit residues: 7.2393 Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2534 Z= 0.256 Angle : 0.442 4.356 3457 Z= 0.236 Chirality : 0.037 0.112 390 Planarity : 0.004 0.034 420 Dihedral : 3.506 12.706 331 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % 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: 1.21 (0.51), residues: 306 helix: 0.95 (0.35), residues: 241 sheet: None (None), residues: 0 loop : 0.66 (0.84), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 243 TYR 0.005 0.001 TYR A 143 PHE 0.007 0.001 PHE A 133 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.191 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.2897 time to fit residues: 7.1919 Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 0.0050 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2534 Z= 0.118 Angle : 0.402 4.265 3457 Z= 0.213 Chirality : 0.035 0.112 390 Planarity : 0.004 0.028 420 Dihedral : 3.307 11.531 331 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % 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: 1.90 (0.51), residues: 306 helix: 1.40 (0.36), residues: 233 sheet: None (None), residues: 0 loop : 1.15 (0.79), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.006 0.001 TYR A 233 PHE 0.006 0.001 PHE A 34 TRP 0.005 0.001 TRP A 247 HIS 0.000 0.000 HIS A 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.165 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.2034 time to fit residues: 5.1780 Evaluate side-chains 22 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2534 Z= 0.268 Angle : 0.456 4.309 3457 Z= 0.246 Chirality : 0.037 0.115 390 Planarity : 0.004 0.027 420 Dihedral : 3.547 13.314 331 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.78 % Allowed : 1.96 % Favored : 97.25 % 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: 1.64 (0.50), residues: 306 helix: 1.25 (0.36), residues: 231 sheet: None (None), residues: 0 loop : 0.92 (0.74), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.007 0.001 TYR A 66 PHE 0.011 0.001 PHE A 133 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.112 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.2308 time to fit residues: 6.6622 Evaluate side-chains 24 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2534 Z= 0.104 Angle : 0.403 4.254 3457 Z= 0.215 Chirality : 0.035 0.118 390 Planarity : 0.004 0.031 420 Dihedral : 3.305 12.150 331 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.51), residues: 306 helix: 1.53 (0.36), residues: 233 sheet: None (None), residues: 0 loop : 1.39 (0.79), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.006 0.001 TYR A 233 PHE 0.007 0.001 PHE A 288 TRP 0.004 0.001 TRP A 231 HIS 0.001 0.000 HIS A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 535.76 seconds wall clock time: 9 minutes 38.15 seconds (578.15 seconds total)