Starting phenix.real_space_refine on Tue Feb 11 04:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri9_19184/02_2025/8ri9_19184.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians C 1290 2.51 5 N 355 2.21 5 O 405 1.98 5 H 2180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4230 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 846 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain breaks: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.33, per 1000 atoms: 0.55 Number of scatterers: 4230 At special positions: 0 Unit cell: (73.01, 63.623, 38.591, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 405 8.00 N 355 7.00 C 1290 6.00 H 2180 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 - 3.00 Amino acid : True - 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: 1.19 Conformation dependent library (CDL) restraints added in 332.8 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 52.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 52 removed outlier: 6.309A pdb=" N THR B 44 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY A 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLU B 46 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL A 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N GLY A 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS B 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL E 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.724A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.414A pdb=" N GLU B 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR A 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN B 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.528A pdb=" N VAL B 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 82 removed outlier: 6.793A pdb=" N ALA B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYS C 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N VAL C 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS D 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL D 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LYS E 80 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN D 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL E 82 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR D 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 96 removed outlier: 6.408A pdb=" N ALA B 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLY A 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR B 92 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N PHE B 94 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 94 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 95 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS C 96 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE D 94 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 95 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS D 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE E 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 95 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) 55 hydrogen bonds defined for protein. 165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.07: 490 1.07 - 1.19: 1690 1.19 - 1.31: 360 1.31 - 1.43: 430 1.43 - 1.55: 1265 Bond restraints: 4235 Sorted by residual: bond pdb=" N VAL B 55 " pdb=" H VAL B 55 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ALA D 53 " pdb=" H ALA D 53 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN B 79 " pdb="HE21 GLN B 79 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLN E 62 " pdb=" H GLN E 62 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL D 52 " pdb=" H VAL D 52 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 4230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 5152 1.64 - 3.28: 1741 3.28 - 4.92: 466 4.92 - 6.57: 297 6.57 - 8.21: 44 Bond angle restraints: 7700 Sorted by residual: angle pdb=" CB HIS A 50 " pdb=" CG HIS A 50 " pdb=" CD2 HIS A 50 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB HIS D 50 " pdb=" CG HIS D 50 " pdb=" CD2 HIS D 50 " ideal model delta sigma weight residual 131.20 125.42 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " pdb=" CD2 HIS C 50 " ideal model delta sigma weight residual 131.20 125.43 5.77 1.30e+00 5.92e-01 1.97e+01 angle pdb=" CB HIS E 50 " pdb=" CG HIS E 50 " pdb=" CD2 HIS E 50 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" CB HIS B 50 " pdb=" CG HIS B 50 " pdb=" CD2 HIS B 50 " ideal model delta sigma weight residual 131.20 125.45 5.75 1.30e+00 5.92e-01 1.95e+01 ... (remaining 7695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1695 16.67 - 33.33: 95 33.33 - 50.00: 20 50.00 - 66.66: 115 66.66 - 83.33: 15 Dihedral angle restraints: 1940 sinusoidal: 1080 harmonic: 860 Sorted by residual: dihedral pdb=" CA THR E 59 " pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA THR B 59 " pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA THR C 59 " pdb=" C THR C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 204 0.053 - 0.105: 106 0.105 - 0.157: 50 0.157 - 0.210: 5 0.210 - 0.262: 5 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA GLU B 83 " pdb=" N GLU B 83 " pdb=" C GLU B 83 " pdb=" CB GLU B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLU C 83 " pdb=" N GLU C 83 " pdb=" C GLU C 83 " pdb=" CB GLU C 83 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLU A 83 " pdb=" N GLU A 83 " pdb=" C GLU A 83 " pdb=" CB GLU A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 367 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 79 " -0.081 2.00e-02 2.50e+03 7.47e-02 8.36e+01 pdb=" CD GLN B 79 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN B 79 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 GLN B 79 " 0.017 2.00e-02 2.50e+03 pdb="HE21 GLN B 79 " 0.089 2.00e-02 2.50e+03 pdb="HE22 GLN B 79 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 79 " -0.081 2.00e-02 2.50e+03 7.45e-02 8.33e+01 pdb=" CD GLN D 79 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN D 79 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 GLN D 79 " 0.017 2.00e-02 2.50e+03 pdb="HE21 GLN D 79 " 0.089 2.00e-02 2.50e+03 pdb="HE22 GLN D 79 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 79 " -0.081 2.00e-02 2.50e+03 7.45e-02 8.33e+01 pdb=" CD GLN E 79 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN E 79 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 GLN E 79 " 0.017 2.00e-02 2.50e+03 pdb="HE21 GLN E 79 " 0.089 2.00e-02 2.50e+03 pdb="HE22 GLN E 79 " -0.116 2.00e-02 2.50e+03 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.18: 309 2.18 - 2.76: 7146 2.76 - 3.34: 11115 3.34 - 3.92: 14710 3.92 - 4.50: 20172 Nonbonded interactions: 53452 Sorted by model distance: nonbonded pdb="HD12 LEU D 38 " pdb="HD21 LEU E 38 " model vdw 1.604 2.440 nonbonded pdb="HD21 LEU B 38 " pdb="HD12 LEU A 38 " model vdw 1.617 2.440 nonbonded pdb="HD12 LEU B 38 " pdb="HD21 LEU C 38 " model vdw 1.628 2.440 nonbonded pdb=" H LYS C 43 " pdb=" O SER D 42 " model vdw 1.642 2.450 nonbonded pdb=" O SER B 42 " pdb=" H LYS A 43 " model vdw 1.651 2.450 ... (remaining 53447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.120 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: 0.090 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.011 0.036 2055 Z= 0.756 Angle : 1.879 5.854 2770 Z= 1.205 Chirality : 0.076 0.262 370 Planarity : 0.009 0.027 335 Dihedral : 12.246 83.327 695 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 0.00 % Favored : 97.62 % 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: -1.61 (0.41), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.009 0.005 PHE B 94 TYR 0.047 0.023 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 31 average time/residue: 0.2076 time to fit residues: 8.3169 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.127210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102380 restraints weight = 7063.509| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.09 r_work: 0.3871 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2055 Z= 0.254 Angle : 0.608 5.405 2770 Z= 0.328 Chirality : 0.051 0.141 370 Planarity : 0.003 0.009 335 Dihedral : 6.833 18.161 290 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.012 0.003 PHE B 94 TYR 0.013 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.248 Fit side-chains REVERT: B 83 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7565 (mp0) REVERT: E 46 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6706 (tt0) REVERT: E 83 GLU cc_start: 0.8355 (mp0) cc_final: 0.7736 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2835 time to fit residues: 6.6015 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 0.0370 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.132743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.107395 restraints weight = 6762.690| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.98 r_work: 0.3963 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2055 Z= 0.120 Angle : 0.466 3.725 2770 Z= 0.254 Chirality : 0.052 0.129 370 Planarity : 0.002 0.006 335 Dihedral : 5.343 15.112 290 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.47), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.003 0.001 PHE B 94 TYR 0.008 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.288 Fit side-chains REVERT: B 83 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7234 (mp0) REVERT: C 83 GLU cc_start: 0.7727 (mp0) cc_final: 0.7228 (mp0) REVERT: E 46 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6685 (tt0) REVERT: E 83 GLU cc_start: 0.8268 (mp0) cc_final: 0.7724 (mp0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.2578 time to fit residues: 5.8702 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.101909 restraints weight = 7032.036| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.02 r_work: 0.3885 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2055 Z= 0.184 Angle : 0.477 3.511 2770 Z= 0.262 Chirality : 0.050 0.123 370 Planarity : 0.002 0.006 335 Dihedral : 5.235 14.196 290 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.48 % Allowed : 6.19 % Favored : 93.33 % 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: -1.70 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 50 PHE 0.006 0.001 PHE C 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.338 Fit side-chains REVERT: B 83 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 83 GLU cc_start: 0.7860 (mp0) cc_final: 0.7427 (mp0) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.2683 time to fit residues: 6.3511 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.125801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.101169 restraints weight = 7124.000| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.00 r_work: 0.3894 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2055 Z= 0.181 Angle : 0.466 3.630 2770 Z= 0.257 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 5.103 13.740 290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -1.88 (0.44), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.006 0.001 PHE B 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.319 Fit side-chains REVERT: B 83 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 83 GLU cc_start: 0.7906 (mp0) cc_final: 0.7381 (mp0) REVERT: E 83 GLU cc_start: 0.8411 (mp0) cc_final: 0.7804 (mp0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.2381 time to fit residues: 5.5576 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.103941 restraints weight = 6954.172| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.98 r_work: 0.3940 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2055 Z= 0.107 Angle : 0.423 3.203 2770 Z= 0.232 Chirality : 0.052 0.125 370 Planarity : 0.001 0.005 335 Dihedral : 4.617 12.819 290 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.48 % Allowed : 6.67 % Favored : 92.86 % 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: -1.63 (0.46), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 50 PHE 0.004 0.001 PHE E 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.285 Fit side-chains REVERT: B 83 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7759 (mt-10) REVERT: E 38 LEU cc_start: 0.5124 (mp) cc_final: 0.4799 (tt) REVERT: E 83 GLU cc_start: 0.8392 (mp0) cc_final: 0.7801 (mp0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.2094 time to fit residues: 5.4229 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.119428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.094073 restraints weight = 7428.835| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.27 r_work: 0.3822 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2055 Z= 0.254 Angle : 0.498 3.665 2770 Z= 0.278 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 5.219 13.974 290 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.48 % Allowed : 6.19 % Favored : 93.33 % 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: -2.06 (0.42), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7761 (mt-10) REVERT: E 38 LEU cc_start: 0.5144 (mp) cc_final: 0.4821 (tt) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1792 time to fit residues: 4.7883 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.097389 restraints weight = 7233.726| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.23 r_work: 0.3874 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2055 Z= 0.137 Angle : 0.437 3.412 2770 Z= 0.241 Chirality : 0.052 0.127 370 Planarity : 0.001 0.006 335 Dihedral : 4.856 12.893 290 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.013 0.002 PHE E 94 TYR 0.008 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 83 GLU cc_start: 0.7747 (mp0) cc_final: 0.7365 (mp0) REVERT: D 46 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 38 LEU cc_start: 0.5156 (mp) cc_final: 0.4856 (tt) REVERT: E 83 GLU cc_start: 0.8397 (mp0) cc_final: 0.7891 (mp0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2066 time to fit residues: 5.3952 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.120666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.095159 restraints weight = 7397.524| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.28 r_work: 0.3849 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2055 Z= 0.175 Angle : 0.457 3.539 2770 Z= 0.253 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 4.902 13.134 290 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.012 0.002 PHE E 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 83 GLU cc_start: 0.7816 (mp0) cc_final: 0.7417 (mp0) REVERT: A 46 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7710 (mt-10) REVERT: D 46 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7445 (mt-10) REVERT: E 38 LEU cc_start: 0.5193 (mp) cc_final: 0.4957 (tt) REVERT: E 83 GLU cc_start: 0.8361 (mp0) cc_final: 0.7820 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2058 time to fit residues: 5.0788 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.118811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093941 restraints weight = 7407.636| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.22 r_work: 0.3826 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2055 Z= 0.216 Angle : 0.476 3.681 2770 Z= 0.265 Chirality : 0.051 0.126 370 Planarity : 0.002 0.006 335 Dihedral : 5.155 14.018 290 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.48 % Allowed : 6.19 % Favored : 93.33 % 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: -2.17 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.012 0.002 PHE E 94 TYR 0.010 0.002 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 83 GLU cc_start: 0.7867 (mp0) cc_final: 0.7441 (mp0) REVERT: E 38 LEU cc_start: 0.5286 (mp) cc_final: 0.5020 (tt) REVERT: E 83 GLU cc_start: 0.8367 (mp0) cc_final: 0.7818 (mp0) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.2114 time to fit residues: 5.5848 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.119933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.094646 restraints weight = 7308.811| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.21 r_work: 0.3829 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2055 Z= 0.199 Angle : 0.470 3.622 2770 Z= 0.261 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 5.134 14.700 290 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.48 % Allowed : 6.67 % Favored : 92.86 % 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: -2.19 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.011 0.002 PHE E 94 TYR 0.009 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.55 seconds wall clock time: 54 minutes 15.88 seconds (3255.88 seconds total)