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/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=True secondary_structure.enabled=False resolution=3.65 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 } 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: 3.91, per 1000 atoms: 0.21 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: 6.50 Conformation dependent library (CDL) restraints added in 816.1 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 7.18 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: 0.100 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: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 26.100 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:25.060 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9876 Z= 0.398 Angle : 0.639 8.678 13471 Z= 0.332 Chirality : 0.064 0.314 1499 Planarity : 0.005 0.048 1739 Dihedral : 12.430 86.620 3532 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.65 % Allowed : 3.97 % Favored : 95.39 % 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: -1.75 (0.23), residues: 1241 helix: -2.42 (0.65), residues: 49 sheet: -0.46 (0.26), residues: 425 loop : -1.53 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.018 0.002 TYR A 201 PHE 0.020 0.002 PHE E 465 TRP 0.014 0.002 TRP C 47 HIS 0.008 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9876 Z= 0.301 Angle : 0.551 8.350 13471 Z= 0.279 Chirality : 0.060 0.207 1499 Planarity : 0.005 0.041 1739 Dihedral : 11.894 87.160 3532 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.83 % Allowed : 5.44 % Favored : 93.73 % 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: -1.70 (0.24), residues: 1241 helix: -2.31 (0.66), residues: 49 sheet: -0.47 (0.27), residues: 406 loop : -1.46 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 543 TYR 0.012 0.001 TYR B 91 PHE 0.016 0.001 PHE E 509 TRP 0.011 0.001 TRP C 47 HIS 0.009 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 90 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9876 Z= 0.326 Angle : 0.576 8.300 13471 Z= 0.296 Chirality : 0.063 0.249 1499 Planarity : 0.005 0.042 1739 Dihedral : 11.769 84.466 3532 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.38 % Allowed : 5.81 % Favored : 92.80 % 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: -1.76 (0.24), residues: 1241 helix: -2.65 (0.62), residues: 55 sheet: -0.55 (0.27), residues: 408 loop : -1.44 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.015 0.002 TYR C 91 PHE 0.018 0.001 PHE E 509 TRP 0.013 0.002 TRP C 47 HIS 0.008 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9876 Z= 0.200 Angle : 0.489 7.711 13471 Z= 0.242 Chirality : 0.059 0.191 1499 Planarity : 0.004 0.038 1739 Dihedral : 11.370 84.382 3532 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.92 % Allowed : 6.00 % Favored : 93.08 % 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: -1.63 (0.24), residues: 1241 helix: -2.56 (0.63), residues: 55 sheet: -0.45 (0.27), residues: 408 loop : -1.35 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.010 0.001 TYR B 91 PHE 0.014 0.001 PHE E 509 TRP 0.009 0.001 TRP C 47 HIS 0.007 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 116 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 overall best weight: 6.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9876 Z= 0.292 Angle : 0.553 8.563 13471 Z= 0.282 Chirality : 0.061 0.194 1499 Planarity : 0.004 0.042 1739 Dihedral : 11.594 81.449 3532 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 1.57 % Allowed : 6.46 % Favored : 91.97 % 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: -1.77 (0.24), residues: 1241 helix: -2.08 (0.74), residues: 48 sheet: -0.55 (0.27), residues: 396 loop : -1.50 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 543 TYR 0.014 0.001 TYR A 201 PHE 0.017 0.001 PHE E 509 TRP 0.012 0.001 TRP C 47 HIS 0.008 0.001 HIS C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 681.31 seconds wall clock time: 12 minutes 27.93 seconds (747.93 seconds total)