Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.pdb" } resolution = 3.0 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= 0.049 sd= 0.288 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 7 5.16 5 C 802 2.51 5 N 228 2.21 5 O 247 1.98 5 H 1238 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 2522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2522 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Time building chain proxies: 0.54, per 1000 atoms: 0.21 Number of scatterers: 2522 At special positions: 0 Unit cell: (65.6731, 58.6866, 65.6731, 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 7 16.00 O 247 8.00 N 228 7.00 C 802 6.00 H 1238 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: 0.44 Conformation dependent library (CDL) restraints added in 74.6 milliseconds 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 71.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.606A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 76 removed outlier: 3.573A pdb=" N HIS A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 124 Processing helix chain 'A' and resid 128 through 158 removed outlier: 4.487A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 261 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: 0.40 Time building geometry restraints manager: 0.52 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: 1235 1.14 - 1.31: 230 1.31 - 1.48: 512 1.48 - 1.64: 559 1.64 - 1.81: 11 Bond restraints: 2547 Sorted by residual: bond pdb=" ND2 ASN A 110 " pdb="HD22 ASN A 110 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N HIS A 129 " pdb=" H HIS A 129 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" NH2 ARG A 23 " pdb="HH22 ARG A 23 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N TYR A 138 " pdb=" H TYR A 138 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" N ASN A 140 " pdb=" H ASN A 140 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.85: 30 106.85 - 113.61: 2943 113.61 - 120.37: 869 120.37 - 127.13: 726 127.13 - 133.89: 13 Bond angle restraints: 4581 Sorted by residual: angle pdb=" C VAL A 9 " pdb=" CA VAL A 9 " pdb=" CB VAL A 9 " ideal model delta sigma weight residual 111.85 109.82 2.03 1.27e+00 6.20e-01 2.56e+00 angle pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta sigma weight residual 122.53 119.70 2.83 1.92e+00 2.71e-01 2.18e+00 angle pdb=" N TYR A 138 " pdb=" CA TYR A 138 " pdb=" C TYR A 138 " ideal model delta sigma weight residual 113.12 114.78 -1.66 1.25e+00 6.40e-01 1.76e+00 angle pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 117.60 119.41 -1.81 1.39e+00 5.18e-01 1.69e+00 angle pdb=" C THR A 136 " pdb=" N HIS A 137 " pdb=" CA HIS A 137 " ideal model delta sigma weight residual 122.60 120.23 2.37 1.88e+00 2.83e-01 1.59e+00 ... (remaining 4576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 1137 16.71 - 33.41: 34 33.41 - 50.12: 15 50.12 - 66.83: 2 66.83 - 83.53: 4 Dihedral angle restraints: 1192 sinusoidal: 640 harmonic: 552 Sorted by residual: dihedral pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 151 " pdb=" C ASP A 151 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " ideal model delta harmonic sigma weight residual 180.00 164.89 15.11 0 5.00e+00 4.00e-02 9.14e+00 dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual 180.00 167.53 12.47 0 5.00e+00 4.00e-02 6.22e+00 ... (remaining 1189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 121 0.024 - 0.049: 44 0.049 - 0.073: 11 0.073 - 0.097: 6 0.097 - 0.121: 3 Chirality restraints: 185 Sorted by residual: chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 182 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 127 " 0.012 5.00e-02 4.00e+02 1.88e-02 5.65e-01 pdb=" N PRO A 128 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 88 " -0.012 5.00e-02 4.00e+02 1.76e-02 4.94e-01 pdb=" N PRO A 89 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " -0.003 2.00e-02 2.50e+03 6.39e-03 4.08e-01 pdb=" C GLU A 28 " 0.011 2.00e-02 2.50e+03 pdb=" O GLU A 28 " -0.004 2.00e-02 2.50e+03 pdb=" N LEU A 29 " -0.004 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 318 2.32 - 2.89: 5436 2.89 - 3.46: 6335 3.46 - 4.03: 7971 4.03 - 4.60: 11995 Nonbonded interactions: 32055 Sorted by model distance: nonbonded pdb=" OD1 ASP A 92 " pdb=" H ASP A 93 " model vdw 1.744 1.850 nonbonded pdb=" O ASP A 132 " pdb=" HG1 THR A 136 " model vdw 1.765 1.850 nonbonded pdb=" O SER A 32 " pdb=" HG SER A 60 " model vdw 1.778 1.850 nonbonded pdb=" H GLN A 15 " pdb=" HG2 GLN A 15 " model vdw 1.820 2.270 nonbonded pdb=" HH TYR A 35 " pdb=" OE2 GLU A 108 " model vdw 1.843 1.850 ... (remaining 32050 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=0.51 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: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.950 Find NCS groups from input model: 0.010 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:4.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:1.760 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1309 Z= 0.178 Angle : 0.455 3.044 1762 Z= 0.276 Chirality : 0.032 0.121 185 Planarity : 0.003 0.019 233 Dihedral : 11.226 83.533 496 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.23 (0.63), residues: 153 helix: 0.88 (0.44), residues: 117 sheet: None (None), residues: 0 loop : -2.19 (0.91), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.010 0.001 TYR A 33 PHE 0.005 0.001 PHE A 133 TRP 0.005 0.001 TRP A 94 HIS 0.002 0.001 HIS A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.063 Fit side-chains REVERT: A 18 GLU cc_start: 0.8581 (tt0) cc_final: 0.8350 (tt0) REVERT: A 44 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8430 (mtm180) REVERT: A 72 LYS cc_start: 0.9102 (tttt) cc_final: 0.8870 (ttpt) REVERT: A 76 GLN cc_start: 0.8349 (tt0) cc_final: 0.8091 (tt0) REVERT: A 120 LYS cc_start: 0.8729 (tttt) cc_final: 0.8418 (ttmp) outliers start: 0 outliers final: 1 residues processed: 43 average time/residue: 1.5474 time to fit residues: 67.2525 Evaluate side-chains 35 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 84 GLN A 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1309 Z= 0.198 Angle : 0.474 4.090 1762 Z= 0.266 Chirality : 0.032 0.119 185 Planarity : 0.003 0.017 233 Dihedral : 6.789 70.796 172 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % 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: 2.81 (0.67), residues: 153 helix: 2.83 (0.45), residues: 119 sheet: None (None), residues: 0 loop : -1.96 (0.96), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 80 TYR 0.020 0.002 TYR A 33 PHE 0.005 0.001 PHE A 133 TRP 0.006 0.002 TRP A 94 HIS 0.004 0.001 HIS A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8112 (tt0) cc_final: 0.7862 (tt0) REVERT: A 44 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8401 (mtm180) REVERT: A 72 LYS cc_start: 0.9074 (tttt) cc_final: 0.8832 (ttpt) REVERT: A 92 ASP cc_start: 0.7242 (t0) cc_final: 0.6519 (m-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 2.5052 time to fit residues: 85.9805 Evaluate side-chains 30 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1309 Z= 0.164 Angle : 0.437 3.234 1762 Z= 0.247 Chirality : 0.031 0.121 185 Planarity : 0.002 0.017 233 Dihedral : 6.367 69.113 170 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % 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: 3.63 (0.67), residues: 153 helix: 3.49 (0.44), residues: 118 sheet: None (None), residues: 0 loop : -1.81 (0.96), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 80 TYR 0.016 0.002 TYR A 33 PHE 0.004 0.001 PHE A 133 TRP 0.004 0.002 TRP A 94 HIS 0.003 0.001 HIS A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.9022 (tttt) cc_final: 0.8763 (ttpt) REVERT: A 120 LYS cc_start: 0.8532 (tttt) cc_final: 0.8312 (ttpm) REVERT: A 141 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8050 (mp0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.7312 time to fit residues: 57.7139 Evaluate side-chains 29 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1309 Z= 0.193 Angle : 0.463 3.261 1762 Z= 0.263 Chirality : 0.032 0.120 185 Planarity : 0.003 0.022 233 Dihedral : 6.253 67.250 170 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.71 % Allowed : 13.57 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.67), residues: 153 helix: 3.49 (0.44), residues: 119 sheet: None (None), residues: 0 loop : -1.44 (0.98), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.016 0.002 TYR A 33 PHE 0.005 0.001 PHE A 42 TRP 0.004 0.002 TRP A 94 HIS 0.004 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.9038 (tttt) cc_final: 0.8800 (ttpt) REVERT: A 141 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8127 (mp0) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 1.5096 time to fit residues: 45.8394 Evaluate side-chains 29 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1309 Z= 0.168 Angle : 0.444 3.276 1762 Z= 0.252 Chirality : 0.031 0.121 185 Planarity : 0.002 0.023 233 Dihedral : 6.137 65.865 170 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % 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: 4.10 (0.67), residues: 153 helix: 3.65 (0.44), residues: 119 sheet: None (None), residues: 0 loop : -1.08 (1.00), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.015 0.002 TYR A 33 PHE 0.006 0.001 PHE A 42 TRP 0.003 0.001 TRP A 94 HIS 0.003 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9245 (ttpp) cc_final: 0.8863 (mmtm) REVERT: A 72 LYS cc_start: 0.9025 (tttt) cc_final: 0.8785 (ttpt) REVERT: A 120 LYS cc_start: 0.8565 (tttt) cc_final: 0.8333 (ttpm) REVERT: A 141 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8204 (mp0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.2443 time to fit residues: 37.7784 Evaluate side-chains 29 residues out of total 140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1309 Z= 0.173 Angle : 0.454 3.373 1762 Z= 0.257 Chirality : 0.031 0.121 185 Planarity : 0.002 0.023 233 Dihedral : 6.027 64.138 170 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % 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: 4.12 (0.67), residues: 153 helix: 3.64 (0.44), residues: 119 sheet: None (None), residues: 0 loop : -0.93 (1.02), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.014 0.002 TYR A 33 PHE 0.007 0.001 PHE A 42 TRP 0.003 0.001 TRP A 94 HIS 0.003 0.001 HIS A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 619.86 seconds wall clock time: 10 minutes 59.17 seconds (659.17 seconds total)