Starting phenix.real_space_refine on Sun May 19 16:31:30 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.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=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.pdb" } resolution = 3.1 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= 0.062 sd= 0.217 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 31 5.16 5 C 4953 2.51 5 N 1242 2.21 5 O 1444 1.98 5 H 7601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 15271 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 11821 Inner-chain residues flagged as termini: ['pdbres="PRO A 248 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="PRO A 652 "', 'pdbres="THR A 698 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 751} Modifications used: {'COO': 6, 'NH2': 2, 'NH3': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1609 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 3.86, per 1000 atoms: 0.25 Number of scatterers: 15271 At special positions: 0 Unit cell: (98.77, 100.43, 146.91, 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 31 16.00 O 1444 8.00 N 1242 7.00 C 4953 6.00 H 7601 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 5.14 Conformation dependent library (CDL) restraints added in 751.8 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 5.71 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: 7590 1.14 - 1.31: 1261 1.31 - 1.48: 3246 1.48 - 1.64: 3308 1.64 - 1.81: 45 Bond restraints: 15450 Sorted by residual: bond pdb=" N ASN L 54 " pdb=" H ASN L 54 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" N SER A 852 " pdb=" H SER A 852 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N ILE A 136 " pdb=" H ILE A 136 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N GLY A 900 " pdb=" H GLY A 900 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N VAL A 812 " pdb=" H VAL A 812 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 15445 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 180 106.34 - 113.25: 18018 113.25 - 120.17: 4851 120.17 - 127.08: 4740 127.08 - 133.99: 89 Bond angle restraints: 27878 Sorted by residual: angle pdb=" N SER A 655 " pdb=" CA SER A 655 " pdb=" CB SER A 655 " ideal model delta sigma weight residual 114.17 110.91 3.26 1.14e+00 7.69e-01 8.18e+00 angle pdb=" C GLU A 426 " pdb=" N GLY A 427 " pdb=" CA GLY A 427 " ideal model delta sigma weight residual 121.03 117.80 3.23 1.51e+00 4.39e-01 4.58e+00 angle pdb=" N GLY A 549 " pdb=" CA GLY A 549 " pdb=" C GLY A 549 " ideal model delta sigma weight residual 113.18 108.43 4.75 2.37e+00 1.78e-01 4.02e+00 angle pdb=" CA SER A 655 " pdb=" C SER A 655 " pdb=" N LYS A 656 " ideal model delta sigma weight residual 119.38 117.14 2.24 1.24e+00 6.50e-01 3.27e+00 angle pdb=" N GLY A 427 " pdb=" CA GLY A 427 " pdb=" C GLY A 427 " ideal model delta sigma weight residual 110.18 112.95 -2.77 1.56e+00 4.11e-01 3.15e+00 ... (remaining 27873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 4831 15.67 - 31.34: 424 31.34 - 47.00: 152 47.00 - 62.67: 74 62.67 - 78.34: 12 Dihedral angle restraints: 5493 sinusoidal: 3858 harmonic: 1635 Sorted by residual: dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N THR H 61 " pdb=" CA THR H 61 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CB LYS A 909 " pdb=" CG LYS A 909 " pdb=" CD LYS A 909 " pdb=" CE LYS A 909 " ideal model delta sinusoidal sigma weight residual -180.00 -125.72 -54.28 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 5490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 724 0.029 - 0.057: 329 0.057 - 0.086: 82 0.086 - 0.114: 54 0.114 - 0.142: 28 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA ILE A 520 " pdb=" N ILE A 520 " pdb=" C ILE A 520 " pdb=" CB ILE A 520 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL A 430 " pdb=" N VAL A 430 " pdb=" C VAL A 430 " pdb=" CB VAL A 430 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1214 not shown) Planarity restraints: 2283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 133 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 112 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 52 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO H 53 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.019 5.00e-02 4.00e+02 ... (remaining 2280 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 873 2.06 - 2.70: 22011 2.70 - 3.33: 44080 3.33 - 3.97: 60211 3.97 - 4.60: 88390 Nonbonded interactions: 215565 Sorted by model distance: nonbonded pdb=" OD1 ASP A 408 " pdb=" HG1 THR A 428 " model vdw 1.429 1.850 nonbonded pdb=" OE1 GLN H 35 " pdb=" HE1 TRP H 47 " model vdw 1.526 1.850 nonbonded pdb="HH21 ARG A 396 " pdb=" O ASP A 435 " model vdw 1.532 1.850 nonbonded pdb=" O PHE A 613 " pdb=" H ILE A 641 " model vdw 1.534 1.850 nonbonded pdb="HD21 ASN A 534 " pdb=" OE1 GLN A 563 " model vdw 1.537 1.850 ... (remaining 215560 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: 0.140 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: 0.150 Extract box with map and model: 0.430 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 21.070 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:19.410 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.023 7849 Z= 0.133 Angle : 0.473 4.750 10661 Z= 0.265 Chirality : 0.042 0.142 1217 Planarity : 0.004 0.045 1340 Dihedral : 11.934 78.340 2758 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 0.12 % Allowed : 0.97 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.33 (0.25), residues: 966 helix: 0.03 (0.25), residues: 341 sheet: 0.02 (0.29), residues: 303 loop : -0.47 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.011 0.001 TYR H 60 PHE 0.011 0.001 PHE A 925 TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS A 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7849 Z= 0.262 Angle : 0.449 4.896 10661 Z= 0.242 Chirality : 0.053 0.205 1217 Planarity : 0.003 0.035 1340 Dihedral : 10.854 77.905 2758 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.12 % Allowed : 0.85 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.27), residues: 966 helix: 0.71 (0.27), residues: 344 sheet: 0.26 (0.29), residues: 308 loop : -0.04 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 906 TYR 0.011 0.001 TYR A 180 PHE 0.011 0.001 PHE A 178 TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7849 Z= 0.263 Angle : 0.447 4.917 10661 Z= 0.239 Chirality : 0.055 0.179 1217 Planarity : 0.003 0.030 1340 Dihedral : 10.427 78.576 2758 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.11 (0.27), residues: 966 helix: 0.61 (0.28), residues: 335 sheet: 0.05 (0.30), residues: 304 loop : -0.25 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 13 TYR 0.009 0.001 TYR A 228 PHE 0.012 0.001 PHE A 223 TRP 0.011 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 0.0010 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7849 Z= 0.214 Angle : 0.389 4.757 10661 Z= 0.206 Chirality : 0.052 0.172 1217 Planarity : 0.003 0.029 1340 Dihedral : 10.085 79.307 2758 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.13 (0.27), residues: 966 helix: 0.66 (0.28), residues: 332 sheet: -0.01 (0.30), residues: 310 loop : -0.16 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.011 0.001 TYR A 180 PHE 0.007 0.001 PHE A 769 TRP 0.009 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 7849 Z= 0.481 Angle : 0.548 4.775 10661 Z= 0.300 Chirality : 0.058 0.195 1217 Planarity : 0.004 0.029 1340 Dihedral : 11.069 87.781 2758 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.48 % Allowed : 3.02 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.09 (0.26), residues: 966 helix: -0.76 (0.26), residues: 332 sheet: -0.50 (0.31), residues: 275 loop : -0.57 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 13 TYR 0.015 0.002 TYR A 180 PHE 0.012 0.002 PHE H 29 TRP 0.017 0.002 TRP A 709 HIS 0.004 0.001 HIS A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7849 Z= 0.119 Angle : 0.365 4.700 10661 Z= 0.191 Chirality : 0.051 0.175 1217 Planarity : 0.003 0.029 1340 Dihedral : 10.127 86.863 2758 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.36 % Allowed : 1.93 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.27), residues: 966 helix: 0.21 (0.28), residues: 327 sheet: -0.32 (0.31), residues: 286 loop : -0.06 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.009 0.001 TYR A 180 PHE 0.009 0.001 PHE A 223 TRP 0.006 0.001 TRP A 709 HIS 0.002 0.000 HIS L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 713.84 seconds wall clock time: 12 minutes 43.01 seconds (763.01 seconds total)