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/8dq0_27645.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.74 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.map" } resolution = 3.74 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= 0.005 sd= 0.378 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2372 atoms to isotropic. 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 14 5.16 5 C 1507 2.51 5 N 440 2.21 5 O 430 1.98 5 H 2362 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 276": "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: 4753 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4753 Classifications: {'peptide': 298} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Time building chain proxies: 0.90, per 1000 atoms: 0.19 Number of scatterers: 4753 At special positions: 0 Unit cell: (63.21, 67.08, 63.21, 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 14 16.00 O 430 8.00 N 440 7.00 C 1507 6.00 H 2362 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: 0.99 Conformation dependent library (CDL) restraints added in 177.7 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 40.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.477A pdb=" N GLU A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 72 through 81 removed outlier: 6.190A pdb=" N LEU A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.506A pdb=" N GLN A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.598A pdb=" N ARG A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.153A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.067A pdb=" N VAL A 90 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 137 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA A 92 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TRP A 34 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP A 65 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 36 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 14 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 16 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLN A 9 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.637A pdb=" N PHE A 166 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU A 151 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU A 144 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 153 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP A 142 " --> pdb=" O VAL A 153 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.14 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: 2353 1.14 - 1.31: 412 1.31 - 1.48: 1000 1.48 - 1.64: 1024 1.64 - 1.81: 19 Bond restraints: 4808 Sorted by residual: bond pdb=" N GLY A 39 " pdb=" H GLY A 39 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N LEU A 277 " pdb=" H LEU A 277 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N ARG A 3 " pdb=" H ARG A 3 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" NH1 ARG A 243 " pdb="HH12 ARG A 243 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N ALA A 6 " pdb=" H ALA A 6 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 4803 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.73: 95 106.73 - 113.54: 5546 113.54 - 120.34: 1581 120.34 - 127.14: 1407 127.14 - 133.95: 46 Bond angle restraints: 8675 Sorted by residual: angle pdb=" C LEU A 78 " pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " ideal model delta sigma weight residual 113.57 109.87 3.70 1.57e+00 4.06e-01 5.55e+00 angle pdb=" C LEU A 77 " pdb=" N LEU A 78 " pdb=" CA LEU A 78 " ideal model delta sigma weight residual 119.83 122.37 -2.54 1.11e+00 8.12e-01 5.23e+00 angle pdb=" CA LEU A 78 " pdb=" C LEU A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 120.58 119.19 1.39 7.40e-01 1.83e+00 3.53e+00 angle pdb=" N PHE A 175 " pdb=" CA PHE A 175 " pdb=" C PHE A 175 " ideal model delta sigma weight residual 109.62 107.26 2.36 1.50e+00 4.44e-01 2.48e+00 angle pdb=" C VAL A 24 " pdb=" N PHE A 25 " pdb=" CA PHE A 25 " ideal model delta sigma weight residual 121.32 118.34 2.98 2.10e+00 2.27e-01 2.01e+00 ... (remaining 8670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2037 17.70 - 35.39: 131 35.39 - 53.09: 44 53.09 - 70.79: 16 70.79 - 88.49: 2 Dihedral angle restraints: 2230 sinusoidal: 1224 harmonic: 1006 Sorted by residual: dihedral pdb=" CA THR A 68 " pdb=" C THR A 68 " pdb=" N HIS A 69 " pdb=" CA HIS A 69 " ideal model delta harmonic sigma weight residual -180.00 -164.33 -15.67 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N ARG A 122 " pdb=" CA ARG A 122 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 dihedral pdb=" CA LEU A 4 " pdb=" C LEU A 4 " pdb=" N SER A 5 " pdb=" CA SER A 5 " ideal model delta harmonic sigma weight residual -180.00 -165.10 -14.90 0 5.00e+00 4.00e-02 8.89e+00 ... (remaining 2227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 223 0.027 - 0.055: 92 0.055 - 0.082: 23 0.082 - 0.109: 15 0.109 - 0.136: 5 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE A 154 " pdb=" N ILE A 154 " pdb=" C ILE A 154 " pdb=" CB ILE A 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 355 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 277 " 0.015 5.00e-02 4.00e+02 2.23e-02 7.93e-01 pdb=" N PRO A 278 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 82 " -0.013 5.00e-02 4.00e+02 2.00e-02 6.39e-01 pdb=" N PRO A 83 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO A 124 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.010 5.00e-02 4.00e+02 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 311 2.15 - 2.77: 8743 2.77 - 3.38: 13568 3.38 - 3.99: 17941 3.99 - 4.60: 27182 Nonbonded interactions: 67745 Sorted by model distance: nonbonded pdb="HH11 ARG A 251 " pdb=" OE2 GLU A 256 " model vdw 1.542 1.850 nonbonded pdb=" O ARG A 148 " pdb="HH12 ARG A 171 " model vdw 1.562 1.850 nonbonded pdb=" H LEU A 143 " pdb=" O LEU A 151 " model vdw 1.585 1.850 nonbonded pdb=" O ASP A 44 " pdb=" H VAL A 48 " model vdw 1.591 1.850 nonbonded pdb=" HH TYR A 72 " pdb=" O PHE A 276 " model vdw 1.593 1.850 ... (remaining 67740 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: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.750 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 0.016 2446 Z= 0.149 Angle : 0.502 4.244 3320 Z= 0.266 Chirality : 0.038 0.136 358 Planarity : 0.003 0.022 435 Dihedral : 13.085 70.891 909 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -1.84 (0.45), residues: 296 helix: -0.22 (0.46), residues: 104 sheet: -3.05 (0.65), residues: 41 loop : -1.33 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.009 0.001 TYR A 238 PHE 0.006 0.001 PHE A 276 TRP 0.003 0.000 TRP A 65 HIS 0.002 0.001 HIS A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7796 (tp30) cc_final: 0.7564 (tp30) REVERT: A 286 MET cc_start: 0.7585 (mmt) cc_final: 0.6715 (mmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1586 time to fit residues: 8.4855 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 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 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2446 Z= 0.270 Angle : 0.496 4.015 3320 Z= 0.252 Chirality : 0.039 0.136 358 Planarity : 0.003 0.024 435 Dihedral : 5.001 38.229 335 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.40 % Allowed : 7.57 % Favored : 92.03 % 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: -1.30 (0.48), residues: 296 helix: 0.60 (0.49), residues: 104 sheet: -3.24 (0.65), residues: 51 loop : -0.94 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.002 TYR A 238 PHE 0.009 0.002 PHE A 276 TRP 0.005 0.001 TRP A 34 HIS 0.002 0.001 HIS A 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7805 (tp30) cc_final: 0.7536 (tp30) REVERT: A 286 MET cc_start: 0.8013 (mmt) cc_final: 0.7172 (mmt) REVERT: A 289 MET cc_start: 0.8065 (ttt) cc_final: 0.7614 (ttt) REVERT: A 293 LEU cc_start: 0.8548 (mm) cc_final: 0.8134 (mm) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.3941 time to fit residues: 17.8195 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2446 Z= 0.313 Angle : 0.507 3.874 3320 Z= 0.264 Chirality : 0.040 0.138 358 Planarity : 0.004 0.024 435 Dihedral : 4.754 20.202 335 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.59 % Allowed : 9.16 % Favored : 89.24 % 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: -1.34 (0.48), residues: 296 helix: 0.72 (0.51), residues: 104 sheet: -3.20 (0.70), residues: 51 loop : -1.12 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.011 0.002 TYR A 238 PHE 0.009 0.002 PHE A 25 TRP 0.006 0.001 TRP A 142 HIS 0.004 0.001 HIS A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7772 (tp30) cc_final: 0.7509 (tp30) REVERT: A 286 MET cc_start: 0.8205 (mmt) cc_final: 0.7692 (mmt) REVERT: A 293 LEU cc_start: 0.8603 (mm) cc_final: 0.8074 (mm) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.2795 time to fit residues: 13.8730 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2446 Z= 0.260 Angle : 0.494 4.315 3320 Z= 0.252 Chirality : 0.039 0.138 358 Planarity : 0.003 0.022 435 Dihedral : 4.655 19.281 335 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.20 % Allowed : 11.55 % Favored : 87.25 % 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: -1.12 (0.50), residues: 296 helix: 0.88 (0.53), residues: 103 sheet: -3.10 (0.73), residues: 51 loop : -0.95 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.009 0.002 TYR A 201 PHE 0.009 0.002 PHE A 276 TRP 0.005 0.001 TRP A 34 HIS 0.002 0.001 HIS A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7880 (tp30) cc_final: 0.7573 (tp30) REVERT: A 286 MET cc_start: 0.8328 (mmt) cc_final: 0.7593 (mmt) REVERT: A 293 LEU cc_start: 0.8608 (mm) cc_final: 0.8068 (mm) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.2374 time to fit residues: 10.8835 Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2446 Z= 0.217 Angle : 0.473 3.962 3320 Z= 0.239 Chirality : 0.038 0.137 358 Planarity : 0.003 0.021 435 Dihedral : 4.493 18.271 335 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.80 % Allowed : 12.35 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.50), residues: 296 helix: 1.05 (0.53), residues: 103 sheet: -2.89 (0.74), residues: 51 loop : -0.93 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.002 TYR A 238 PHE 0.008 0.001 PHE A 276 TRP 0.005 0.001 TRP A 129 HIS 0.002 0.001 HIS A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.7728 (m-30) cc_final: 0.7392 (m-30) REVERT: A 31 GLU cc_start: 0.7870 (tp30) cc_final: 0.7556 (tp30) REVERT: A 286 MET cc_start: 0.8337 (mmt) cc_final: 0.7660 (mmt) REVERT: A 293 LEU cc_start: 0.8622 (mm) cc_final: 0.8070 (mm) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.2135 time to fit residues: 9.2472 Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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: 0.7468 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2446 Z= 0.192 Angle : 0.464 4.306 3320 Z= 0.232 Chirality : 0.038 0.140 358 Planarity : 0.003 0.021 435 Dihedral : 4.383 17.195 335 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.40 % Allowed : 12.75 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.51), residues: 296 helix: 1.22 (0.54), residues: 103 sheet: -2.71 (0.76), residues: 51 loop : -0.83 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.008 0.002 TYR A 201 PHE 0.006 0.001 PHE A 25 TRP 0.004 0.001 TRP A 129 HIS 0.002 0.001 HIS A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 590.86 seconds wall clock time: 10 minutes 33.45 seconds (633.45 seconds total)