Starting phenix.real_space_refine on Sun May 19 16:31:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False resolution=3.65 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb" } resolution = 3.65 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 ramachandran_plot_restraints { enabled = 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= 0.011 sd= 0.089 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 53 5.16 5 C 6044 2.51 5 N 1646 2.21 5 O 1884 1.98 5 H 9288 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 139": "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: 18915 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4331 Classifications: {'peptide': 284} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 260} Chain: "H" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3307 Inner-chain residues flagged as termini: ['pdbres="SER H 127 "', 'pdbres="SER H 132 "'] Classifications: {'peptide': 225} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3244 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1225 Inner-chain residues flagged as termini: ['pdbres="THR A 255 "', 'pdbres="PRO A 295 "'] Classifications: {'peptide': 82} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain breaks: 1 Chain: "B" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3191 Inner-chain residues flagged as termini: ['pdbres="GLY B 128 "'] Classifications: {'peptide': 211} Modifications used: {'COO': 1, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain: "C" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3617 Classifications: {'peptide': 242} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Time building chain proxies: 3.66, per 1000 atoms: 0.19 Number of scatterers: 18915 At special positions: 0 Unit cell: (72.009, 139.573, 139.573, 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 53 16.00 O 1884 8.00 N 1646 7.00 C 6044 6.00 H 9288 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 429 " - pdb=" SG CYS E 503 " distance=2.03 Simple disulfide: pdb=" SG CYS E 452 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS E 486 " distance=2.04 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 564 " distance=2.04 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 552 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 597 " distance=2.03 Simple disulfide: pdb=" SG CYS E 581 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 607 " - pdb=" SG CYS E 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 677 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.05 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: 4.86 Conformation dependent library (CDL) restraints added in 635.6 milliseconds Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.15: 9288 1.15 - 1.33: 1699 1.33 - 1.50: 4305 1.50 - 1.68: 3808 1.68 - 1.86: 64 Bond restraints: 19164 Sorted by residual: bond pdb=" NH1 ARG B 141 " pdb="HH12 ARG B 141 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" NH2 ARG C 19 " pdb="HH21 ARG C 19 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" CE1 TYR L 49 " pdb=" HE1 TYR L 49 " ideal model delta sigma weight residual 0.930 1.102 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" CE2 TYR H 99 " pdb=" HE2 TYR H 99 " ideal model delta sigma weight residual 0.930 1.102 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" NH1 ARG B 141 " pdb="HH11 ARG B 141 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.13e+01 ... (remaining 19159 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.16: 256 105.16 - 112.38: 21756 112.38 - 119.60: 4758 119.60 - 126.82: 7576 126.82 - 134.03: 190 Bond angle restraints: 34536 Sorted by residual: angle pdb=" N ALA H 88 " pdb=" CA ALA H 88 " pdb=" C ALA H 88 " ideal model delta sigma weight residual 107.73 114.31 -6.58 1.61e+00 3.86e-01 1.67e+01 angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 107.19 6.71 1.80e+00 3.09e-01 1.39e+01 angle pdb=" C ARG E 587 " pdb=" N LYS E 588 " pdb=" CA LYS E 588 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C SER C 179 " pdb=" N SER C 180 " pdb=" CA SER C 180 " ideal model delta sigma weight residual 121.75 116.83 4.92 1.73e+00 3.34e-01 8.09e+00 angle pdb=" N ARG B 141 " pdb=" CA ARG B 141 " pdb=" C ARG B 141 " ideal model delta sigma weight residual 110.35 114.11 -3.76 1.38e+00 5.25e-01 7.42e+00 ... (remaining 34531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 6072 18.40 - 36.81: 617 36.81 - 55.21: 225 55.21 - 73.61: 30 73.61 - 92.02: 11 Dihedral angle restraints: 6955 sinusoidal: 4989 harmonic: 1966 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -138.44 52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS E 569 " pdb=" SG CYS E 569 " pdb=" SG CYS E 597 " pdb=" CB CYS E 597 " ideal model delta sinusoidal sigma weight residual 93.00 143.64 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS E 452 " pdb=" SG CYS E 452 " pdb=" SG CYS E 620 " pdb=" CB CYS E 620 " ideal model delta sinusoidal sigma weight residual -86.00 -130.46 44.46 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 6952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 933 0.034 - 0.068: 381 0.068 - 0.102: 104 0.102 - 0.136: 71 0.136 - 0.170: 10 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA VAL C 181 " pdb=" N VAL C 181 " pdb=" C VAL C 181 " pdb=" CB VAL C 181 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL H 11 " pdb=" N VAL H 11 " pdb=" C VAL H 11 " pdb=" CB VAL H 11 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1496 not shown) Planarity restraints: 2906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.022 2.00e-02 2.50e+03 1.60e-02 7.65e+00 pdb=" CG TYR H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TYR H 99 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR H 99 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.028 2.00e-02 2.50e+03 1.53e-02 6.98e+00 pdb=" CG TYR L 49 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR L 49 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 49 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR L 49 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 99 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C TYR H 99 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR H 99 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS H 100 " 0.014 2.00e-02 2.50e+03 ... (remaining 2903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1071 2.08 - 2.71: 28299 2.71 - 3.34: 51424 3.34 - 3.97: 69438 3.97 - 4.60: 101113 Nonbonded interactions: 251345 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" HG1 THR A 255 " model vdw 1.452 1.850 nonbonded pdb=" O ASN E 540 " pdb="HD21 ASN E 548 " model vdw 1.455 1.850 nonbonded pdb=" O SER B 127 " pdb=" H1 GLY B 128 " model vdw 1.479 1.960 nonbonded pdb=" O ASP E 658 " pdb=" HG SER E 678 " model vdw 1.490 1.850 nonbonded pdb=" OD1 ASP L 170 " pdb=" HG1 THR L 172 " model vdw 1.507 1.850 ... (remaining 251340 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: 0.060 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: 0.180 Extract box with map and model: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 18.640 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:22.080 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9876 Z= 0.215 Angle : 0.641 6.709 13471 Z= 0.341 Chirality : 0.045 0.170 1499 Planarity : 0.005 0.057 1739 Dihedral : 12.887 92.017 3532 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.65 % Allowed : 2.21 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.83 (0.23), residues: 1241 helix: -3.01 (0.56), residues: 48 sheet: -0.60 (0.25), residues: 444 loop : -1.50 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 77 TYR 0.039 0.002 TYR H 99 PHE 0.009 0.001 PHE E 509 TRP 0.016 0.001 TRP C 154 HIS 0.006 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9876 Z= 0.280 Angle : 0.562 5.383 13471 Z= 0.290 Chirality : 0.060 0.209 1499 Planarity : 0.005 0.048 1739 Dihedral : 12.261 87.187 3532 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.17 % Favored : 86.78 % Rotamer: Outliers : 0.92 % Allowed : 2.86 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.22), residues: 1241 helix: -3.52 (0.50), residues: 48 sheet: -1.47 (0.24), residues: 415 loop : -2.52 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.015 0.002 TYR A 201 PHE 0.016 0.001 PHE E 465 TRP 0.014 0.002 TRP C 47 HIS 0.007 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 60.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 27 optimal weight: 7.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9876 Z= 0.444 Angle : 0.669 8.110 13471 Z= 0.353 Chirality : 0.066 0.220 1499 Planarity : 0.006 0.068 1739 Dihedral : 12.581 89.594 3532 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 4.43 % Allowed : 17.24 % Favored : 78.32 % Rotamer: Outliers : 1.75 % Allowed : 7.10 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.02 (0.19), residues: 1241 helix: -3.70 (0.45), residues: 49 sheet: -2.66 (0.24), residues: 376 loop : -3.90 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 38 TYR 0.019 0.002 TYR A 201 PHE 0.017 0.002 PHE E 509 TRP 0.015 0.002 TRP C 47 HIS 0.012 0.002 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 90 optimal weight: 50.0000 overall best weight: 9.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9876 Z= 0.367 Angle : 0.603 9.090 13471 Z= 0.314 Chirality : 0.063 0.218 1499 Planarity : 0.005 0.062 1739 Dihedral : 12.468 89.222 3532 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 4.43 % Allowed : 17.97 % Favored : 77.60 % Rotamer: Outliers : 2.68 % Allowed : 7.47 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.37 (0.18), residues: 1241 helix: -3.85 (0.41), residues: 49 sheet: -3.05 (0.22), residues: 386 loop : -4.07 (0.17), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 100G TYR 0.012 0.002 TYR B 91 PHE 0.019 0.002 PHE E 509 TRP 0.012 0.002 TRP C 103 HIS 0.009 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 9 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 100.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9876 Z= 0.375 Angle : 0.593 7.741 13471 Z= 0.307 Chirality : 0.063 0.202 1499 Planarity : 0.005 0.058 1739 Dihedral : 12.445 88.985 3532 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 5.24 % Allowed : 19.10 % Favored : 75.66 % Rotamer: Outliers : 2.68 % Allowed : 8.03 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.74 (0.18), residues: 1241 helix: -4.26 (0.34), residues: 49 sheet: -3.35 (0.23), residues: 364 loop : -4.29 (0.16), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 100G TYR 0.016 0.002 TYR A 201 PHE 0.019 0.002 PHE E 509 TRP 0.010 0.002 TRP C 47 HIS 0.010 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9876 Z= 0.437 Angle : 0.657 7.692 13471 Z= 0.347 Chirality : 0.065 0.223 1499 Planarity : 0.006 0.062 1739 Dihedral : 12.721 88.392 3532 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 6.45 % Allowed : 21.11 % Favored : 72.44 % Rotamer: Outliers : 3.97 % Allowed : 9.13 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -6.08 (0.18), residues: 1241 helix: -4.41 (0.32), residues: 49 sheet: -3.72 (0.22), residues: 352 loop : -4.47 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 543 TYR 0.014 0.002 TYR A 201 PHE 0.021 0.002 PHE E 509 TRP 0.014 0.002 TRP C 103 HIS 0.011 0.001 HIS C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 381.63 seconds wall clock time: 7 minutes 35.72 seconds (455.72 seconds total)