Starting phenix.real_space_refine on Sun May 19 16:31:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False resolution=3.67 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map" } resolution = 3.67 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { secondary_structure { enabled = False } c_beta_restraints = False } 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= 0.031 sd= 0.268 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 57 5.16 5 C 5307 2.51 5 N 1431 2.21 5 O 1577 1.98 5 H 8296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 16668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11116 Inner-chain residues flagged as termini: ['pdbres="PHE A 167 "', 'pdbres="VAL A 234 "'] Classifications: {'peptide': 681} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2394 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3158 Classifications: {'peptide': 202} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 186} Time building chain proxies: 4.39, per 1000 atoms: 0.26 Number of scatterers: 16668 At special positions: 0 Unit cell: (118.44, 110.88, 109.62, 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 57 16.00 O 1577 8.00 N 1431 7.00 C 5307 6.00 H 8296 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: 5.99 Conformation dependent library (CDL) restraints added in 946.7 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 8267 1.15 - 1.31: 1437 1.31 - 1.48: 3387 1.48 - 1.65: 3669 1.65 - 1.81: 85 Bond restraints: 16845 Sorted by residual: bond pdb=" N LEU A 849 " pdb=" H LEU A 849 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ASN A 258 " pdb=" H ASN A 258 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N ASP A 389 " pdb=" H ASP A 389 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N LYS B 115 " pdb=" H LYS B 115 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N PHE A 612 " pdb=" H PHE A 612 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 ... (remaining 16840 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.92: 202 105.92 - 112.92: 19472 112.92 - 119.93: 4806 119.93 - 126.93: 5855 126.93 - 133.94: 83 Bond angle restraints: 30418 Sorted by residual: angle pdb=" C PRO A 745 " pdb=" N LEU A 746 " pdb=" CA LEU A 746 " ideal model delta sigma weight residual 120.79 123.38 -2.59 1.39e+00 5.18e-01 3.49e+00 angle pdb=" CA TYR A 494 " pdb=" CB TYR A 494 " pdb=" CG TYR A 494 " ideal model delta sigma weight residual 113.90 117.05 -3.15 1.80e+00 3.09e-01 3.06e+00 angle pdb=" CA VAL A 740 " pdb=" C VAL A 740 " pdb=" N THR A 741 " ideal model delta sigma weight residual 116.60 119.07 -2.47 1.45e+00 4.76e-01 2.90e+00 angle pdb=" CA TRP A 791 " pdb=" CB TRP A 791 " pdb=" CG TRP A 791 " ideal model delta sigma weight residual 113.60 110.52 3.08 1.90e+00 2.77e-01 2.63e+00 angle pdb=" CB ARG C 196 " pdb=" CG ARG C 196 " pdb=" CD ARG C 196 " ideal model delta sigma weight residual 111.30 114.94 -3.64 2.30e+00 1.89e-01 2.50e+00 ... (remaining 30413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5435 17.29 - 34.58: 379 34.58 - 51.87: 132 51.87 - 69.16: 33 69.16 - 86.45: 5 Dihedral angle restraints: 5984 sinusoidal: 4370 harmonic: 1614 Sorted by residual: dihedral pdb=" CA ARG C 209 " pdb=" CB ARG C 209 " pdb=" CG ARG C 209 " pdb=" CD ARG C 209 " ideal model delta sinusoidal sigma weight residual 60.00 117.00 -57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " pdb=" CG ARG A 155 " pdb=" CD ARG A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -114.03 54.03 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 529 " pdb=" CB ARG A 529 " pdb=" CG ARG A 529 " pdb=" CD ARG A 529 " ideal model delta sinusoidal sigma weight residual -180.00 -128.92 -51.08 3 1.50e+01 4.44e-03 8.97e+00 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 834 0.031 - 0.061: 302 0.061 - 0.092: 70 0.092 - 0.122: 45 0.122 - 0.153: 9 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL C 157 " pdb=" N VAL C 157 " pdb=" C VAL C 157 " pdb=" CB VAL C 157 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1257 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 307 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.131 9.50e-02 1.11e+02 4.38e-02 2.10e+00 pdb=" NE ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 141 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO C 142 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.017 5.00e-02 4.00e+02 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 875 2.06 - 2.70: 23987 2.70 - 3.33: 50031 3.33 - 3.97: 64113 3.97 - 4.60: 95622 Nonbonded interactions: 234628 Sorted by model distance: nonbonded pdb="HE21 GLN A 410 " pdb=" O GLU A 415 " model vdw 1.429 1.850 nonbonded pdb=" H SER B 118 " pdb=" OE1 GLU B 121 " model vdw 1.480 1.850 nonbonded pdb=" O LEU A 770 " pdb=" HG1 THR A 774 " model vdw 1.523 1.850 nonbonded pdb=" O GLY A 154 " pdb=" HG SER A 158 " model vdw 1.563 1.850 nonbonded pdb=" OE1 GLU A 860 " pdb=" HE ARG A 861 " model vdw 1.571 1.850 ... (remaining 234623 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: 0.020 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: 0.120 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 25.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:22.860 Internal consistency checks: 0.000 Total: 49.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8549 Z= 0.121 Angle : 0.506 3.884 11554 Z= 0.281 Chirality : 0.038 0.153 1260 Planarity : 0.005 0.057 1505 Dihedral : 10.847 77.471 3280 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.32 % Allowed : 2.34 % Favored : 97.35 % 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: -0.54 (0.25), residues: 1017 helix: -0.35 (0.21), residues: 483 sheet: -0.55 (0.47), residues: 117 loop : -0.04 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.016 0.001 TYR A 494 PHE 0.018 0.002 PHE A 730 TRP 0.011 0.002 TRP A 791 HIS 0.004 0.001 HIS C 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 8549 Z= 0.257 Angle : 0.666 5.403 11554 Z= 0.360 Chirality : 0.058 0.219 1260 Planarity : 0.006 0.055 1505 Dihedral : 10.928 71.918 3280 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.64 % Allowed : 3.08 % Favored : 96.28 % 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: -1.02 (0.25), residues: 1017 helix: -0.86 (0.22), residues: 478 sheet: -0.97 (0.48), residues: 120 loop : -0.05 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 138 TYR 0.021 0.002 TYR A 624 PHE 0.023 0.002 PHE A 601 TRP 0.015 0.002 TRP A 600 HIS 0.004 0.001 HIS A 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8549 Z= 0.137 Angle : 0.443 4.432 11554 Z= 0.226 Chirality : 0.049 0.156 1260 Planarity : 0.004 0.048 1505 Dihedral : 10.305 69.349 3280 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.53 % Allowed : 2.87 % Favored : 96.60 % 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: -0.37 (0.26), residues: 1017 helix: -0.30 (0.24), residues: 474 sheet: -0.93 (0.49), residues: 120 loop : 0.33 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.010 0.001 TYR B 88 PHE 0.012 0.001 PHE A 256 TRP 0.009 0.001 TRP B 139 HIS 0.002 0.001 HIS C 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 40.0000 chunk 77 optimal weight: 0.0370 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 overall best weight: 2.4862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8549 Z= 0.092 Angle : 0.395 4.550 11554 Z= 0.198 Chirality : 0.047 0.153 1260 Planarity : 0.004 0.041 1505 Dihedral : 9.480 67.620 3280 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.42 % Allowed : 2.76 % Favored : 96.82 % 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: 0.38 (0.27), residues: 1017 helix: 0.39 (0.24), residues: 464 sheet: -0.82 (0.49), residues: 118 loop : 0.71 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 734 TYR 0.009 0.001 TYR B 86 PHE 0.008 0.001 PHE A 256 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.000 HIS C 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8549 Z= 0.124 Angle : 0.432 4.514 11554 Z= 0.221 Chirality : 0.048 0.152 1260 Planarity : 0.004 0.046 1505 Dihedral : 9.558 70.479 3280 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.74 % Allowed : 2.76 % Favored : 96.50 % 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: 0.29 (0.27), residues: 1017 helix: 0.30 (0.25), residues: 452 sheet: -1.00 (0.48), residues: 116 loop : 0.70 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 267 TYR 0.010 0.001 TYR A 624 PHE 0.010 0.001 PHE A 599 TRP 0.008 0.001 TRP B 139 HIS 0.002 0.001 HIS A 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.1980 chunk 7 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 8549 Z= 0.058 Angle : 0.359 4.360 11554 Z= 0.174 Chirality : 0.045 0.154 1260 Planarity : 0.003 0.036 1505 Dihedral : 8.997 68.208 3280 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 2.34 % Favored : 97.03 % 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: 0.88 (0.27), residues: 1017 helix: 0.81 (0.25), residues: 457 sheet: -0.86 (0.48), residues: 118 loop : 1.04 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 267 TYR 0.007 0.001 TYR B 86 PHE 0.006 0.001 PHE A 467 TRP 0.006 0.001 TRP B 139 HIS 0.002 0.000 HIS C 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 768.81 seconds wall clock time: 13 minutes 44.77 seconds (824.77 seconds total)