Starting phenix.real_space_refine on Thu Mar 6 00:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri9_19184/03_2025/8ri9_19184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri9_19184/03_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_19184/03_2025/8ri9_19184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri9_19184/03_2025/8ri9_19184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri9_19184/03_2025/8ri9_19184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri9_19184/03_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-5624/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: 1.91, per 1000 atoms: 0.45 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: 1.34 Conformation dependent library (CDL) restraints added in 347.7 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: 0.50 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: 1.31 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: 0.480 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: 0.070 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- 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 : 0.293 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 31 average time/residue: 0.1699 time to fit residues: 6.8955 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 : 0.282 ------------------------------------------------------------------------------- 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 = 0.127211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102396 restraints weight = 7063.485| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.09 r_work: 0.3869 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 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 5.406 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 : 0.282 Fit side-chains REVERT: B 83 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7566 (mp0) REVERT: E 46 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6709 (tt0) REVERT: E 83 GLU cc_start: 0.8356 (mp0) cc_final: 0.7738 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2479 time to fit residues: 5.8984 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 : 0.280 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.123602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.097818 restraints weight = 7149.420| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.19 r_work: 0.3867 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.3135 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= 0.195 Angle : 0.504 3.843 2770 Z= 0.277 Chirality : 0.051 0.126 370 Planarity : 0.002 0.007 335 Dihedral : 5.653 15.288 290 Min Nonbonded Distance : 2.598 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: -1.81 (0.44), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.003 0.001 PHE B 94 TYR 0.011 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 : 0.417 Fit side-chains REVERT: B 83 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7289 (mp0) REVERT: C 83 GLU cc_start: 0.7850 (mp0) cc_final: 0.7325 (mp0) REVERT: E 46 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7072 (mt-10) REVERT: E 83 GLU cc_start: 0.8242 (mp0) cc_final: 0.7631 (mp0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.3076 time to fit residues: 6.8076 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 : 0.354 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.126780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.101843 restraints weight = 7077.329| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.08 r_work: 0.3890 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.3451 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= 0.166 Angle : 0.463 3.435 2770 Z= 0.254 Chirality : 0.051 0.123 370 Planarity : 0.002 0.006 335 Dihedral : 5.183 13.945 290 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: -1.84 (0.44), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.006 0.001 PHE C 94 TYR 0.009 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 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.394 Fit side-chains REVERT: B 83 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 83 GLU cc_start: 0.7931 (mp0) cc_final: 0.7466 (mp0) REVERT: D 46 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 46 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6911 (mt-10) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.2331 time to fit residues: 6.3621 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 : 0.598 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.118387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.094608 restraints weight = 7676.420| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.19 r_work: 0.3775 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2055 Z= 0.341 Angle : 0.577 4.144 2770 Z= 0.323 Chirality : 0.050 0.124 370 Planarity : 0.003 0.007 335 Dihedral : 5.901 15.184 290 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % 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: -2.72 (0.39), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.009 0.002 PHE B 94 TYR 0.014 0.003 TYR D 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 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.326 Fit side-chains REVERT: B 46 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7300 (mt-10) REVERT: B 83 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7714 (mt-10) REVERT: C 83 GLU cc_start: 0.7929 (mp0) cc_final: 0.7615 (mp0) REVERT: A 83 GLU cc_start: 0.8231 (mp0) cc_final: 0.7754 (mp0) REVERT: E 46 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6846 (mt-10) REVERT: E 83 GLU cc_start: 0.8116 (mp0) cc_final: 0.7628 (mp0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1974 time to fit residues: 5.7216 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 : 0.291 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.124015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.100009 restraints weight = 7148.739| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.00 r_work: 0.3857 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2055 Z= 0.149 Angle : 0.468 3.735 2770 Z= 0.258 Chirality : 0.052 0.126 370 Planarity : 0.002 0.005 335 Dihedral : 5.193 14.354 290 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.95 % Allowed : 6.19 % 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: -2.23 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.005 0.001 PHE B 94 TYR 0.010 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: 2 poor density : 18 time to evaluate : 0.391 Fit side-chains REVERT: B 46 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 83 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 83 GLU cc_start: 0.7896 (mp0) cc_final: 0.7282 (mp0) REVERT: D 46 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7482 (mt-10) REVERT: E 38 LEU cc_start: 0.4835 (mp) cc_final: 0.4573 (tt) REVERT: E 46 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6850 (mt-10) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.3124 time to fit residues: 8.2630 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 : 0.689 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.113256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.089992 restraints weight = 8046.337| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.21 r_work: 0.3837 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2055 Z= 0.342 Angle : 0.575 4.137 2770 Z= 0.322 Chirality : 0.050 0.126 370 Planarity : 0.003 0.007 335 Dihedral : 5.853 14.881 290 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 0.95 % Allowed : 5.71 % 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: -2.97 (0.39), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.29), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.009 0.002 PHE B 94 TYR 0.013 0.003 TYR D 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 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.609 Fit side-chains REVERT: B 39 TYR cc_start: 0.6065 (t80) cc_final: 0.5700 (t80) REVERT: B 83 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 83 GLU cc_start: 0.7985 (mp0) cc_final: 0.7675 (mp0) REVERT: D 46 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 38 LEU cc_start: 0.5274 (mp) cc_final: 0.4942 (tt) REVERT: E 46 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6899 (mt-10) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1873 time to fit residues: 5.6869 Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094434 restraints weight = 7510.612| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.19 r_work: 0.3875 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2055 Z= 0.158 Angle : 0.495 5.653 2770 Z= 0.273 Chirality : 0.053 0.137 370 Planarity : 0.002 0.005 335 Dihedral : 5.297 17.276 290 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.48 % Allowed : 5.71 % 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: -2.45 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 50 PHE 0.004 0.001 PHE B 94 TYR 0.010 0.002 TYR D 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 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.335 Fit side-chains REVERT: B 83 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 83 GLU cc_start: 0.7847 (mp0) cc_final: 0.7249 (mp0) REVERT: D 46 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7454 (mt-10) REVERT: E 38 LEU cc_start: 0.5209 (mp) cc_final: 0.4935 (tt) REVERT: E 46 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6848 (mt-10) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.2553 time to fit residues: 6.3626 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 THR 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: 4.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.114952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.090765 restraints weight = 7762.291| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.24 r_work: 0.3873 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.4093 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= 0.208 Angle : 0.508 4.493 2770 Z= 0.282 Chirality : 0.051 0.128 370 Planarity : 0.002 0.006 335 Dihedral : 5.295 16.092 290 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.48 % Allowed : 5.71 % 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: -2.53 (0.41), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.006 0.001 PHE B 94 TYR 0.011 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 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.364 Fit side-chains REVERT: B 83 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 83 GLU cc_start: 0.7970 (mp0) cc_final: 0.7668 (mp0) REVERT: D 46 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7431 (mt-10) REVERT: E 38 LEU cc_start: 0.5306 (mp) cc_final: 0.5058 (tt) REVERT: E 46 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6927 (mt-10) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.2025 time to fit residues: 5.4511 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.115581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.091400 restraints weight = 7674.679| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.24 r_work: 0.3884 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.4148 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= 0.207 Angle : 0.500 3.907 2770 Z= 0.277 Chirality : 0.052 0.139 370 Planarity : 0.002 0.007 335 Dihedral : 5.346 16.516 290 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.48 % Allowed : 5.71 % 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: -2.64 (0.41), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.006 0.001 PHE B 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 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.406 Fit side-chains REVERT: B 46 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 83 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 83 GLU cc_start: 0.7954 (mp0) cc_final: 0.7666 (mp0) REVERT: D 46 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7427 (mt-10) REVERT: E 46 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6907 (mt-10) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.2270 time to fit residues: 5.7892 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.120739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.095674 restraints weight = 7344.104| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.25 r_work: 0.3854 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4214 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= 0.167 Angle : 0.477 3.685 2770 Z= 0.263 Chirality : 0.052 0.134 370 Planarity : 0.002 0.007 335 Dihedral : 5.084 16.668 290 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.48 % Allowed : 5.71 % 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: -2.54 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.010 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.68 seconds wall clock time: 56 minutes 19.05 seconds (3379.05 seconds total)