Starting phenix.real_space_refine on Wed Sep 17 04:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri9_19184/09_2025/8ri9_19184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri9_19184/09_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_19184/09_2025/8ri9_19184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri9_19184/09_2025/8ri9_19184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri9_19184/09_2025/8ri9_19184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri9_19184/09_2025/8ri9_19184.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4230 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" 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, A, D, E Time building chain proxies: 0.84, per 1000 atoms: 0.20 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: 0.37 Conformation dependent library (CDL) restraints added in 104.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.14 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: 0.91 Time building geometry restraints manager: 0.54 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' selection = chain 'D' selection = chain 'E' } 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: 0.670 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.310 Find NCS groups from input model: 0.030 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.690 ------------------------------------------------------------------------------- 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= 0.692 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.047 0.023 TYR E 39 PHE 0.009 0.005 PHE B 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01101 ( 2055) covalent geometry : angle 1.87870 ( 2770) hydrogen bonds : bond 0.10336 ( 55) hydrogen bonds : angle 6.73005 ( 165) *********************** 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 : 0.118 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 31 average time/residue: 0.0646 time to fit residues: 2.6730 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 : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.106025 restraints weight = 6886.646| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.01 r_work: 0.3922 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2055 Z= 0.114 Angle : 0.562 5.162 2770 Z= 0.299 Chirality : 0.052 0.146 370 Planarity : 0.002 0.010 335 Dihedral : 6.495 17.814 290 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 39 PHE 0.011 0.003 PHE C 94 HIS 0.003 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2055) covalent geometry : angle 0.56228 ( 2770) hydrogen bonds : bond 0.02451 ( 55) hydrogen bonds : angle 4.15805 ( 165) *********************** 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 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.099 Fit side-chains REVERT: B 46 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 83 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7533 (mp0) REVERT: E 46 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6651 (tt0) REVERT: E 83 GLU cc_start: 0.8297 (mp0) cc_final: 0.7694 (mp0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1032 time to fit residues: 2.3001 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 : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.130706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.105423 restraints weight = 6813.798| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.02 r_work: 0.3932 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.3146 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= 0.114 Angle : 0.470 3.488 2770 Z= 0.257 Chirality : 0.051 0.124 370 Planarity : 0.002 0.006 335 Dihedral : 5.244 15.216 290 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.46), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.002 0.001 PHE E 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 2055) covalent geometry : angle 0.47041 ( 2770) hydrogen bonds : bond 0.01625 ( 55) hydrogen bonds : angle 3.41226 ( 165) *********************** 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 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.092 Fit side-chains REVERT: B 83 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7274 (mp0) REVERT: C 83 GLU cc_start: 0.7698 (mp0) cc_final: 0.7209 (mp0) REVERT: E 46 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7024 (mt-10) REVERT: E 83 GLU cc_start: 0.8190 (mp0) cc_final: 0.7869 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0860 time to fit residues: 2.1517 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.123436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099123 restraints weight = 7146.818| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.99 r_work: 0.3826 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2055 Z= 0.178 Angle : 0.503 3.682 2770 Z= 0.277 Chirality : 0.050 0.123 370 Planarity : 0.002 0.006 335 Dihedral : 5.446 14.822 290 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.43), 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 TYR 0.011 0.002 TYR B 39 PHE 0.011 0.002 PHE E 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2055) covalent geometry : angle 0.50255 ( 2770) hydrogen bonds : bond 0.01909 ( 55) hydrogen bonds : angle 3.40221 ( 165) *********************** 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 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.091 Fit side-chains REVERT: B 83 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 83 GLU cc_start: 0.7850 (mp0) cc_final: 0.7403 (mp0) REVERT: E 83 GLU cc_start: 0.8209 (mp0) cc_final: 0.7996 (mp0) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0895 time to fit residues: 2.4095 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.120735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.094995 restraints weight = 7243.401| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.28 r_work: 0.3838 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.3664 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= 0.155 Angle : 0.480 3.649 2770 Z= 0.265 Chirality : 0.051 0.125 370 Planarity : 0.002 0.005 335 Dihedral : 5.249 15.277 290 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.43), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 39 PHE 0.011 0.002 PHE E 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2055) covalent geometry : angle 0.48017 ( 2770) hydrogen bonds : bond 0.01701 ( 55) hydrogen bonds : angle 3.35289 ( 165) *********************** 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 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.083 Fit side-chains REVERT: B 83 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 83 GLU cc_start: 0.7872 (mp0) cc_final: 0.7247 (mp0) REVERT: D 46 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7484 (mt-10) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0890 time to fit residues: 2.3174 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.125831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.101428 restraints weight = 7218.367| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.03 r_work: 0.3888 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3793 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= 0.100 Angle : 0.449 3.504 2770 Z= 0.246 Chirality : 0.052 0.127 370 Planarity : 0.002 0.014 335 Dihedral : 4.921 14.130 290 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.012 0.001 PHE E 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 2055) covalent geometry : angle 0.44893 ( 2770) hydrogen bonds : bond 0.01463 ( 55) hydrogen bonds : angle 3.31029 ( 165) *********************** 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 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.128 Fit side-chains REVERT: B 83 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 83 GLU cc_start: 0.7794 (mp0) cc_final: 0.7221 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0890 time to fit residues: 2.2170 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 : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.124650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.100630 restraints weight = 7409.071| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.08 r_work: 0.3852 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.3894 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= 0.150 Angle : 0.472 3.538 2770 Z= 0.261 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 5.025 14.425 290 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.44), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.011 0.002 PHE E 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2055) covalent geometry : angle 0.47157 ( 2770) hydrogen bonds : bond 0.01606 ( 55) hydrogen bonds : angle 3.29802 ( 165) *********************** 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 : 0.129 Fit side-chains REVERT: B 83 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 83 GLU cc_start: 0.7919 (mp0) cc_final: 0.7603 (mp0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0691 time to fit residues: 1.9117 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.0010 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.099529 restraints weight = 7079.643| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.22 r_work: 0.3909 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.3995 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= 0.086 Angle : 0.432 3.292 2770 Z= 0.237 Chirality : 0.053 0.135 370 Planarity : 0.001 0.005 335 Dihedral : 4.679 14.989 290 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.47), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.010 0.001 PHE E 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 2055) covalent geometry : angle 0.43181 ( 2770) hydrogen bonds : bond 0.01392 ( 55) hydrogen bonds : angle 3.26620 ( 165) *********************** 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 : 0.089 Fit side-chains REVERT: B 46 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7160 (mt-10) REVERT: B 83 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7639 (mt-10) REVERT: C 83 GLU cc_start: 0.7922 (mp0) cc_final: 0.7588 (mp0) REVERT: E 38 LEU cc_start: 0.5108 (mp) cc_final: 0.4769 (tt) REVERT: E 83 GLU cc_start: 0.8231 (mp0) cc_final: 0.7888 (mp0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0900 time to fit residues: 2.2679 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 : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.096871 restraints weight = 7377.412| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.26 r_work: 0.3866 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4036 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= 0.136 Angle : 0.458 3.430 2770 Z= 0.253 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 4.872 14.619 290 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.008 0.002 TYR D 39 PHE 0.011 0.002 PHE E 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2055) covalent geometry : angle 0.45833 ( 2770) hydrogen bonds : bond 0.01525 ( 55) hydrogen bonds : angle 3.25458 ( 165) *********************** 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: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 83 GLU cc_start: 0.8006 (mp0) cc_final: 0.7670 (mp0) REVERT: A 46 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7698 (mt-10) REVERT: E 38 LEU cc_start: 0.5156 (mp) cc_final: 0.4854 (tt) REVERT: E 83 GLU cc_start: 0.8300 (mp0) cc_final: 0.7897 (mp0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1045 time to fit residues: 2.6329 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 : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.097042 restraints weight = 7258.090| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.22 r_work: 0.3866 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.4104 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= 0.130 Angle : 0.454 3.473 2770 Z= 0.251 Chirality : 0.052 0.126 370 Planarity : 0.002 0.006 335 Dihedral : 4.936 14.440 290 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.011 0.002 PHE E 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 2055) covalent geometry : angle 0.45397 ( 2770) hydrogen bonds : bond 0.01513 ( 55) hydrogen bonds : angle 3.33163 ( 165) ********************** 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: 0 poor density : 19 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 83 GLU cc_start: 0.7911 (mp0) cc_final: 0.7614 (mp0) REVERT: E 38 LEU cc_start: 0.5174 (mp) cc_final: 0.4909 (tt) REVERT: E 83 GLU cc_start: 0.8294 (mp0) cc_final: 0.7914 (mp0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1153 time to fit residues: 2.7109 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 : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.096585 restraints weight = 7201.729| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.22 r_work: 0.3868 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 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 0.020 2055 Z= 0.136 Angle : 0.462 3.534 2770 Z= 0.255 Chirality : 0.051 0.125 370 Planarity : 0.002 0.006 335 Dihedral : 4.964 14.005 290 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.45), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.011 0.002 PHE E 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2055) covalent geometry : angle 0.46228 ( 2770) hydrogen bonds : bond 0.01487 ( 55) hydrogen bonds : angle 3.35112 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.05 seconds wall clock time: 28 minutes 8.12 seconds (1688.12 seconds total)