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/8vi4_43248.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.map" } 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= 0.016 sd= 0.077 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 2489 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: 4942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4942 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.92, per 1000 atoms: 0.19 Number of scatterers: 4942 At special positions: 0 Unit cell: (61.694, 58.864, 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 2489 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: 1.15 Conformation dependent library (CDL) restraints added in 148.0 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 83.4% 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 removed outlier: 3.599A pdb=" N PHE A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 35 through 65 removed outlier: 4.006A pdb=" N ARG A 38 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 65 " --> pdb=" O LYS A 62 " (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 191 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 195 through 218 removed outlier: 4.264A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.709A pdb=" N VAL A 212 " --> 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: 3.984A pdb=" N PHE A 262 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 178 hydrogen bonds defined for protein. 309 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: 1.30 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: 2488 1.14 - 1.31: 356 1.31 - 1.48: 1110 1.48 - 1.64: 1052 1.64 - 1.81: 17 Bond restraints: 5023 Sorted by residual: bond pdb=" N GLY A 256 " pdb=" H GLY A 256 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" N LEU A 92 " pdb=" H LEU A 92 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N PHE A 14 " pdb=" H PHE A 14 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" N ALA A 273 " pdb=" H ALA A 273 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 157 107.23 - 113.92: 5714 113.92 - 120.61: 1939 120.61 - 127.30: 1232 127.30 - 133.98: 38 Bond angle restraints: 9080 Sorted by residual: angle pdb=" N GLY A 94 " pdb=" CA GLY A 94 " pdb=" C GLY A 94 " ideal model delta sigma weight residual 112.64 110.72 1.92 1.21e+00 6.83e-01 2.51e+00 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 109.34 106.53 2.81 2.08e+00 2.31e-01 1.82e+00 angle pdb=" N PHE A 28 " pdb=" CA PHE A 28 " pdb=" C PHE A 28 " ideal model delta sigma weight residual 112.54 111.06 1.48 1.22e+00 6.72e-01 1.47e+00 angle pdb=" C ILE A 86 " pdb=" N PRO A 87 " pdb=" CD PRO A 87 " ideal model delta sigma weight residual 125.00 129.58 -4.58 4.10e+00 5.95e-02 1.25e+00 angle pdb=" C ILE A 16 " pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 125.00 129.54 -4.54 4.10e+00 5.95e-02 1.23e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 2164 14.24 - 28.47: 129 28.47 - 42.71: 40 42.71 - 56.94: 37 56.94 - 71.17: 7 Dihedral angle restraints: 2377 sinusoidal: 1211 harmonic: 1166 Sorted by residual: dihedral pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sinusoidal sigma weight residual -60.00 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+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 -107.39 47.39 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " pdb=" CD GLU A 134 " pdb=" OE1 GLU A 134 " ideal model delta sinusoidal sigma weight residual 0.00 -71.17 71.17 1 3.00e+01 1.11e-03 7.22e+00 ... (remaining 2374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 225 0.022 - 0.044: 93 0.044 - 0.066: 26 0.066 - 0.088: 33 0.088 - 0.109: 13 Chirality restraints: 390 Sorted by residual: 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 2.99e-01 chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 102 " pdb=" N PRO A 102 " pdb=" C PRO A 102 " pdb=" CB PRO A 102 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.39e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 206 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 207 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 45 " -0.005 2.00e-02 2.50e+03 9.52e-03 9.07e-01 pdb=" C GLY A 45 " 0.016 2.00e-02 2.50e+03 pdb=" O GLY A 45 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE A 46 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " -0.005 2.00e-02 2.50e+03 9.42e-03 8.87e-01 pdb=" C LEU A 44 " 0.016 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.005 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 358 2.14 - 2.75: 8692 2.75 - 3.37: 15112 3.37 - 3.98: 19734 3.98 - 4.60: 29848 Nonbonded interactions: 73744 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.523 1.850 nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.568 1.850 nonbonded pdb=" HE1 TRP A 258 " pdb=" OG1 THR A 302 " model vdw 1.574 1.850 nonbonded pdb=" O TRP A 258 " pdb=" HG SER A 261 " model vdw 1.584 1.850 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.589 1.850 ... (remaining 73739 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: 0.020 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: 0.220 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.870 Find NCS groups from input model: 0.040 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.860 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 0.014 2534 Z= 0.120 Angle : 0.437 4.582 3457 Z= 0.234 Chirality : 0.035 0.109 390 Planarity : 0.004 0.028 420 Dihedral : 11.297 71.175 856 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.78 % Allowed : 0.00 % Favored : 99.22 % 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: -1.31 (0.49), residues: 306 helix: -0.82 (0.33), residues: 244 sheet: None (None), residues: 0 loop : -0.21 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.009 0.001 TYR A 304 PHE 0.008 0.001 PHE A 34 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 29 *********************** 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 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.0651 time to fit residues: 1.9276 Evaluate side-chains 18 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 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 101 ASN A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2534 Z= 0.221 Angle : 0.458 4.869 3457 Z= 0.239 Chirality : 0.037 0.112 390 Planarity : 0.004 0.023 420 Dihedral : 5.413 57.686 333 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.18 % Allowed : 1.57 % 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: -0.74 (0.50), residues: 306 helix: -0.41 (0.34), residues: 245 sheet: None (None), residues: 0 loop : -0.06 (0.88), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.006 0.001 TYR A 143 PHE 0.012 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS A 139 *********************** 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 24 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.202 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.1695 time to fit residues: 4.9448 Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 10.0000 chunk 9 optimal weight: 6.9990 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: 8.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 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 29 HIS A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2534 Z= 0.256 Angle : 0.458 4.868 3457 Z= 0.241 Chirality : 0.037 0.117 390 Planarity : 0.005 0.025 420 Dihedral : 5.151 54.713 333 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.78 % Allowed : 2.35 % Favored : 96.86 % 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: -0.48 (0.50), residues: 306 helix: -0.23 (0.34), residues: 245 sheet: None (None), residues: 0 loop : 0.03 (0.89), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.007 0.001 TYR A 304 PHE 0.011 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS A 139 *********************** 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 23 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.198 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1567 time to fit residues: 4.6119 Evaluate side-chains 22 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 101 ASN A 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2534 Z= 0.176 Angle : 0.434 4.702 3457 Z= 0.226 Chirality : 0.036 0.111 390 Planarity : 0.005 0.026 420 Dihedral : 4.842 53.465 333 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.78 % Allowed : 2.75 % Favored : 96.47 % 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: -0.19 (0.50), residues: 306 helix: -0.01 (0.35), residues: 245 sheet: None (None), residues: 0 loop : 0.03 (0.87), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.007 0.001 TYR A 233 PHE 0.006 0.001 PHE A 82 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 163 *********************** 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: 2 poor density : 20 time to evaluate : 0.205 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1360 time to fit residues: 3.9331 Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1666 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= 0.154 Angle : 0.425 4.642 3457 Z= 0.221 Chirality : 0.036 0.110 390 Planarity : 0.005 0.026 420 Dihedral : 4.714 52.229 333 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % 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: -0.04 (0.51), residues: 306 helix: 0.08 (0.35), residues: 245 sheet: None (None), residues: 0 loop : 0.19 (0.88), residues: 61 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 0.005 0.001 PHE A 34 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 29 *********************** 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 23 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.114 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1583 time to fit residues: 4.3964 Evaluate side-chains 21 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2534 Z= 0.113 Angle : 0.411 4.510 3457 Z= 0.212 Chirality : 0.035 0.109 390 Planarity : 0.004 0.027 420 Dihedral : 4.579 51.215 333 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % 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: 0.71 (0.52), residues: 306 helix: 0.46 (0.37), residues: 235 sheet: None (None), residues: 0 loop : 1.06 (0.84), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 79 TYR 0.006 0.001 TYR A 59 PHE 0.004 0.001 PHE A 209 TRP 0.004 0.000 TRP A 247 HIS 0.000 0.000 HIS A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 548.31 seconds wall clock time: 9 minutes 50.51 seconds (590.51 seconds total)