Starting phenix.real_space_refine on Thu Jul 2 06:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.map" model { file = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t03_40933/07_2026/8t03_40933.cif" } resolution = 2.72 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= 0.002 sd= 0.094 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, E, F Time building chain proxies: 1.40, per 1000 atoms: 0.20 Number of scatterers: 6878 At special positions: 0 Unit cell: (92.13, 103.75, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1246 8.00 N 1092 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 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: 0.47 Conformation dependent library (CDL) restraints added in 323.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 41.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.975A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 62 through 87 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.516A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1038 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: 0.99 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1145 1.33 - 1.45: 1929 1.45 - 1.57: 3908 1.57 - 1.69: 4 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.00e-02 1.00e+04 1.37e+01 bond pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.00e-02 1.00e+04 1.33e+01 bond pdb=" N LEU B 10 " pdb=" CA LEU B 10 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.33e+01 bond pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.42e-02 4.96e+03 1.24e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 7570 2.25 - 4.50: 1874 4.50 - 6.75: 114 6.75 - 9.00: 4 9.00 - 11.25: 2 Bond angle restraints: 9564 Sorted by residual: angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.50 -7.12 1.37e+00 5.33e-01 2.70e+01 angle pdb=" C PHE C 54 " pdb=" N TRP C 55 " pdb=" CA TRP C 55 " ideal model delta sigma weight residual 120.38 127.48 -7.10 1.37e+00 5.33e-01 2.68e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.24 117.94 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.24 117.97 4.27 8.70e-01 1.32e+00 2.41e+01 angle pdb=" CA GLY D 101 " pdb=" C GLY D 101 " pdb=" O GLY D 101 " ideal model delta sigma weight residual 122.29 118.46 3.83 8.10e-01 1.52e+00 2.24e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4014 35.87 - 71.74: 90 71.74 - 107.61: 4 107.61 - 143.48: 2 143.48 - 179.35: 4 Dihedral angle restraints: 4114 sinusoidal: 1652 harmonic: 2462 Sorted by residual: dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 38.51 -38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA GLU B 90 " pdb=" C GLU B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 0.00 38.43 -38.43 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" C1 LBN B 303 " pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O3 LBN B 303 " ideal model delta sinusoidal sigma weight residual 275.40 96.05 179.35 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 1052 0.970 - 1.939: 0 1.939 - 2.909: 0 2.909 - 3.879: 0 3.879 - 4.848: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 303 " -0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN B 303 " 0.038 2.00e-02 2.50e+03 pdb=" C5 LBN B 303 " 0.039 2.00e-02 2.50e+03 pdb=" C8 LBN B 303 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 303 " 0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN A 303 " -0.038 2.00e-02 2.50e+03 pdb=" C5 LBN A 303 " -0.039 2.00e-02 2.50e+03 pdb=" C8 LBN A 303 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 90 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 91 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.026 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 33 2.60 - 3.18: 5347 3.18 - 3.75: 10509 3.75 - 4.33: 15424 4.33 - 4.90: 26178 Nonbonded interactions: 57491 Sorted by model distance: nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 97 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 97 " model vdw 2.029 3.760 nonbonded pdb=" OD1 ASP D 28 " pdb=" O GLY D 68 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 28 " pdb=" O GLY F 68 " model vdw 2.206 3.040 nonbonded pdb=" CE1 TYR D 86 " pdb=" CD1 LEU D 104 " model vdw 2.395 3.760 ... (remaining 57486 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.700 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.790 Find NCS groups from input model: 0.040 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.015 0.208 7066 Z= 1.050 Angle : 1.758 11.254 9568 Z= 1.287 Chirality : 0.227 4.848 1054 Planarity : 0.004 0.051 1156 Dihedral : 16.348 179.354 2536 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 4.90 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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 are not related in a simple way. whole: -0.46 (0.29), residues: 840 helix: -0.62 (0.26), residues: 294 sheet: 0.45 (0.39), residues: 196 loop : -0.27 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 168 TYR 0.027 0.003 TYR F 71 PHE 0.022 0.003 PHE A 46 TRP 0.029 0.003 TRP E 110 HIS 0.008 0.002 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.01374 / 1.04 ( 7058) covalent geometry : angle 1.75848 / 1.29 ( 9564) SS BOND : bond 0.00908 / 0.46 ( 2) SS BOND : angle 0.89766 / 0.47 ( 4) hydrogen bonds : bond 0.17264 / 11.26 ( 374) hydrogen bonds : angle 8.60404 / 6.20 ( 1038) metal coordination : bond 0.17156 / 9.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.157 Fit side-chains REVERT: A 29 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7076 (mtp180) REVERT: A 61 MET cc_start: 0.7701 (mtm) cc_final: 0.7328 (mtp) REVERT: A 134 LEU cc_start: 0.7325 (mt) cc_final: 0.7024 (mm) REVERT: A 138 LYS cc_start: 0.6890 (mptt) cc_final: 0.6518 (mptt) REVERT: A 139 GLU cc_start: 0.6813 (tt0) cc_final: 0.6455 (tt0) REVERT: B 29 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7089 (mtp180) REVERT: B 61 MET cc_start: 0.7670 (mtm) cc_final: 0.7320 (mtp) REVERT: B 134 LEU cc_start: 0.7320 (mt) cc_final: 0.7023 (mm) REVERT: B 138 LYS cc_start: 0.6891 (mptt) cc_final: 0.6506 (mptt) REVERT: B 139 GLU cc_start: 0.6827 (tt0) cc_final: 0.6470 (tt0) REVERT: C 41 LYS cc_start: 0.7093 (tttt) cc_final: 0.6753 (ttpp) REVERT: C 61 TYR cc_start: 0.8446 (m-80) cc_final: 0.8099 (m-80) REVERT: C 112 GLN cc_start: 0.7583 (tt0) cc_final: 0.7178 (tt0) REVERT: D 31 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6359 (mp0) REVERT: D 42 LYS cc_start: 0.7527 (mtpp) cc_final: 0.6803 (mtmt) REVERT: E 41 LYS cc_start: 0.7062 (tttt) cc_final: 0.6705 (ttpp) REVERT: E 61 TYR cc_start: 0.8424 (m-80) cc_final: 0.8081 (m-80) REVERT: E 83 MET cc_start: 0.6350 (mmm) cc_final: 0.6123 (mpt) REVERT: F 31 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6297 (mp0) REVERT: F 42 LYS cc_start: 0.7644 (mtpp) cc_final: 0.6966 (mtmt) outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 0.4439 time to fit residues: 62.7011 Evaluate side-chains 100 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117056 restraints weight = 7005.818| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.50 r_work: 0.3079 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7066 Z= 0.133 Angle : 0.595 6.413 9568 Z= 0.309 Chirality : 0.043 0.147 1054 Planarity : 0.004 0.034 1156 Dihedral : 13.468 169.567 1014 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 8.72 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 0.99 (0.30), residues: 840 helix: 1.58 (0.28), residues: 304 sheet: 0.65 (0.35), residues: 230 loop : -0.17 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.012 0.001 TYR F 91 PHE 0.018 0.002 PHE B 39 TRP 0.015 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7058) covalent geometry : angle 0.59544 / 0.31 ( 9564) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 0.53237 / 0.27 ( 4) hydrogen bonds : bond 0.04419 / 2.94 ( 374) hydrogen bonds : angle 5.17424 / 3.74 ( 1038) metal coordination : bond 0.00166 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.189 Fit side-chains REVERT: A 27 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7713 (mttt) REVERT: A 139 GLU cc_start: 0.7862 (tt0) cc_final: 0.7609 (tt0) REVERT: B 27 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7771 (mttt) REVERT: B 139 GLU cc_start: 0.7849 (tt0) cc_final: 0.7598 (tt0) REVERT: D 31 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8057 (mp0) REVERT: D 42 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7903 (mtmm) REVERT: D 45 ARG cc_start: 0.8266 (mtm180) cc_final: 0.8021 (mtp180) REVERT: E 41 LYS cc_start: 0.7897 (tttt) cc_final: 0.7667 (ttpp) REVERT: F 31 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8009 (mp0) REVERT: F 42 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7858 (mtmm) REVERT: F 67 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.6975 (p) outliers start: 19 outliers final: 5 residues processed: 125 average time/residue: 0.5122 time to fit residues: 67.2032 Evaluate side-chains 114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112150 restraints weight = 6994.200| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.07 r_work: 0.3071 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7066 Z= 0.126 Angle : 0.558 6.311 9568 Z= 0.286 Chirality : 0.042 0.140 1054 Planarity : 0.004 0.032 1156 Dihedral : 12.460 178.731 1006 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.59 % Allowed : 12.53 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.35 (0.30), residues: 840 helix: 1.90 (0.28), residues: 306 sheet: 0.71 (0.34), residues: 240 loop : 0.10 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.012 0.001 TYR D 91 PHE 0.016 0.002 PHE A 46 TRP 0.014 0.001 TRP C 110 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7058) covalent geometry : angle 0.55769 / 0.29 ( 9564) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.25560 / 0.14 ( 4) hydrogen bonds : bond 0.04283 / 2.85 ( 374) hydrogen bonds : angle 4.86794 / 3.52 ( 1038) metal coordination : bond 0.00212 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.181 Fit side-chains REVERT: A 27 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7758 (mttt) REVERT: A 139 GLU cc_start: 0.7884 (tt0) cc_final: 0.7597 (tt0) REVERT: B 27 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7844 (mttt) REVERT: B 138 LYS cc_start: 0.7797 (mptt) cc_final: 0.7538 (mptt) REVERT: B 139 GLU cc_start: 0.7890 (tt0) cc_final: 0.7598 (tt0) REVERT: C 41 LYS cc_start: 0.8180 (tttp) cc_final: 0.7571 (tptp) REVERT: D 31 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8116 (mp0) REVERT: D 42 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7916 (mtmm) REVERT: D 45 ARG cc_start: 0.8275 (mtm180) cc_final: 0.8059 (mtp180) REVERT: F 31 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8021 (mp0) REVERT: F 42 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7869 (mtmm) outliers start: 19 outliers final: 5 residues processed: 111 average time/residue: 0.5382 time to fit residues: 62.5725 Evaluate side-chains 108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 112 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115296 restraints weight = 7020.676| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.03 r_work: 0.3038 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7066 Z= 0.133 Angle : 0.548 6.292 9568 Z= 0.281 Chirality : 0.042 0.142 1054 Planarity : 0.005 0.039 1156 Dihedral : 11.736 174.999 1006 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.45 % Allowed : 13.22 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.54 (0.30), residues: 840 helix: 2.14 (0.28), residues: 304 sheet: 0.92 (0.35), residues: 240 loop : 0.00 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.012 0.001 TYR D 86 PHE 0.016 0.002 PHE B 39 TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7058) covalent geometry : angle 0.54795 / 0.28 ( 9564) SS BOND : bond 0.00007 / 0.00 ( 2) SS BOND : angle 0.14312 / 0.08 ( 4) hydrogen bonds : bond 0.04255 / 2.83 ( 374) hydrogen bonds : angle 4.70688 / 3.40 ( 1038) metal coordination : bond 0.00218 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.183 Fit side-chains REVERT: A 27 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7871 (mttt) REVERT: A 139 GLU cc_start: 0.7925 (tt0) cc_final: 0.7650 (tt0) REVERT: B 27 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7868 (mttt) REVERT: B 138 LYS cc_start: 0.7791 (mptt) cc_final: 0.7487 (mptt) REVERT: B 139 GLU cc_start: 0.7929 (tt0) cc_final: 0.7667 (tt0) REVERT: C 41 LYS cc_start: 0.8203 (tttp) cc_final: 0.7700 (tptm) REVERT: C 48 GLU cc_start: 0.8186 (tt0) cc_final: 0.7977 (tt0) REVERT: D 5 THR cc_start: 0.7704 (m) cc_final: 0.7486 (p) REVERT: D 31 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8148 (mp0) REVERT: D 42 LYS cc_start: 0.8336 (mtpp) cc_final: 0.7943 (mtmm) REVERT: D 45 ARG cc_start: 0.8260 (mtm180) cc_final: 0.8053 (mtp180) REVERT: E 48 GLU cc_start: 0.8205 (tt0) cc_final: 0.7997 (tt0) REVERT: F 31 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8073 (mp0) REVERT: F 42 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7877 (mtmm) outliers start: 18 outliers final: 10 residues processed: 112 average time/residue: 0.5965 time to fit residues: 69.9245 Evaluate side-chains 110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 45 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116160 restraints weight = 7102.150| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.89 r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7066 Z= 0.127 Angle : 0.532 6.243 9568 Z= 0.274 Chirality : 0.041 0.137 1054 Planarity : 0.005 0.045 1156 Dihedral : 11.490 179.907 1006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.00 % Allowed : 13.62 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.68 (0.30), residues: 840 helix: 2.20 (0.28), residues: 306 sheet: 1.09 (0.36), residues: 240 loop : 0.04 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.011 0.001 TYR D 91 PHE 0.016 0.002 PHE B 69 TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7058) covalent geometry : angle 0.53198 / 0.27 ( 9564) SS BOND : bond 0.00004 / 0.00 ( 2) SS BOND : angle 0.14578 / 0.08 ( 4) hydrogen bonds : bond 0.04162 / 2.77 ( 374) hydrogen bonds : angle 4.61755 / 3.34 ( 1038) metal coordination : bond 0.00220 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.265 Fit side-chains REVERT: A 27 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8051 (mttt) REVERT: A 139 GLU cc_start: 0.7992 (tt0) cc_final: 0.7727 (tt0) REVERT: B 27 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8053 (mttt) REVERT: B 138 LYS cc_start: 0.7869 (mptt) cc_final: 0.7650 (mptt) REVERT: B 139 GLU cc_start: 0.7995 (tt0) cc_final: 0.7755 (tt0) REVERT: B 166 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: C 41 LYS cc_start: 0.8260 (tttp) cc_final: 0.7898 (tptp) REVERT: C 48 GLU cc_start: 0.8206 (tt0) cc_final: 0.8003 (tt0) REVERT: D 31 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8209 (mp0) REVERT: D 42 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8018 (mtmm) REVERT: D 45 ARG cc_start: 0.8313 (mtm180) cc_final: 0.8014 (mtp180) REVERT: D 61 ARG cc_start: 0.7494 (ptp90) cc_final: 0.7224 (ptp90) REVERT: E 48 GLU cc_start: 0.8246 (tt0) cc_final: 0.8041 (tt0) REVERT: F 31 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8176 (mp0) REVERT: F 42 LYS cc_start: 0.8377 (mtpp) cc_final: 0.7965 (mtmm) outliers start: 22 outliers final: 9 residues processed: 110 average time/residue: 0.5704 time to fit residues: 65.9211 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN D 30 ASN D 49 HIS F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112327 restraints weight = 7049.976| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.93 r_work: 0.3009 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7066 Z= 0.220 Angle : 0.625 6.719 9568 Z= 0.318 Chirality : 0.045 0.150 1054 Planarity : 0.005 0.049 1156 Dihedral : 11.433 169.782 1006 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 14.58 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.45 (0.30), residues: 840 helix: 1.91 (0.28), residues: 302 sheet: 0.95 (0.35), residues: 240 loop : 0.08 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 107 TYR 0.015 0.002 TYR D 86 PHE 0.021 0.002 PHE A 69 TRP 0.017 0.002 TRP E 110 HIS 0.005 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 7058) covalent geometry : angle 0.62460 / 0.32 ( 9564) SS BOND : bond 0.00119 / 0.06 ( 2) SS BOND : angle 0.34381 / 0.19 ( 4) hydrogen bonds : bond 0.05036 / 3.37 ( 374) hydrogen bonds : angle 4.94660 / 3.57 ( 1038) metal coordination : bond 0.00362 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.253 Fit side-chains REVERT: A 27 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7739 (mttt) REVERT: A 63 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7542 (mtp85) REVERT: A 139 GLU cc_start: 0.7865 (tt0) cc_final: 0.7581 (tt0) REVERT: A 166 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7794 (mmm) REVERT: B 27 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7735 (mttt) REVERT: B 139 GLU cc_start: 0.7899 (tt0) cc_final: 0.7627 (tt0) REVERT: B 166 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: C 41 LYS cc_start: 0.8235 (tttp) cc_final: 0.8002 (ttpp) REVERT: C 48 GLU cc_start: 0.8266 (tt0) cc_final: 0.8045 (tt0) REVERT: D 31 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8152 (mp0) REVERT: D 42 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7876 (mtmm) REVERT: F 31 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8123 (mp0) REVERT: F 42 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7908 (mtmm) REVERT: F 61 ARG cc_start: 0.7074 (ptt180) cc_final: 0.6580 (ptp90) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.5166 time to fit residues: 66.5197 Evaluate side-chains 119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 45 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110969 restraints weight = 6997.887| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.11 r_work: 0.3062 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7066 Z= 0.118 Angle : 0.537 6.191 9568 Z= 0.274 Chirality : 0.041 0.136 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.947 167.485 1006 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.45 % Allowed : 14.31 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.68 (0.30), residues: 840 helix: 2.21 (0.28), residues: 304 sheet: 1.11 (0.35), residues: 240 loop : 0.01 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 68 TYR 0.011 0.001 TYR D 86 PHE 0.016 0.002 PHE A 39 TRP 0.012 0.001 TRP C 110 HIS 0.004 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7058) covalent geometry : angle 0.53737 / 0.27 ( 9564) SS BOND : bond 0.00034 / 0.02 ( 2) SS BOND : angle 0.12693 / 0.07 ( 4) hydrogen bonds : bond 0.04079 / 2.72 ( 374) hydrogen bonds : angle 4.59487 / 3.32 ( 1038) metal coordination : bond 0.00164 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.184 Fit side-chains REVERT: A 27 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7771 (mttt) REVERT: A 139 GLU cc_start: 0.7876 (tt0) cc_final: 0.7595 (tt0) REVERT: B 27 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7773 (mttt) REVERT: B 139 GLU cc_start: 0.7878 (tt0) cc_final: 0.7617 (tt0) REVERT: B 166 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7765 (mmm) REVERT: C 41 LYS cc_start: 0.8176 (tttp) cc_final: 0.7939 (ttpp) REVERT: C 48 GLU cc_start: 0.8163 (tt0) cc_final: 0.7941 (tt0) REVERT: D 31 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8087 (mp0) REVERT: D 42 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7848 (mtmm) REVERT: F 31 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8085 (mp0) REVERT: F 42 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7768 (mtmm) outliers start: 18 outliers final: 5 residues processed: 118 average time/residue: 0.5335 time to fit residues: 65.8029 Evaluate side-chains 107 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 0.0000 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN D 30 ASN E 16 GLN E 112 GLN F 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114272 restraints weight = 7092.418| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.39 r_work: 0.3071 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7066 Z= 0.127 Angle : 0.541 6.304 9568 Z= 0.276 Chirality : 0.041 0.138 1054 Planarity : 0.005 0.051 1156 Dihedral : 10.736 162.647 1006 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.59 % Allowed : 14.31 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.74 (0.30), residues: 840 helix: 2.22 (0.28), residues: 304 sheet: 1.17 (0.35), residues: 240 loop : 0.07 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 61 TYR 0.011 0.001 TYR D 86 PHE 0.017 0.002 PHE B 39 TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7058) covalent geometry : angle 0.54137 / 0.28 ( 9564) SS BOND : bond 0.00008 / 0.00 ( 2) SS BOND : angle 0.07436 / 0.04 ( 4) hydrogen bonds : bond 0.04181 / 2.79 ( 374) hydrogen bonds : angle 4.57921 / 3.30 ( 1038) metal coordination : bond 0.00204 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.194 Fit side-chains REVERT: A 27 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7704 (mttt) REVERT: A 139 GLU cc_start: 0.7826 (tt0) cc_final: 0.7537 (tt0) REVERT: A 166 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7635 (mmm) REVERT: B 27 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7707 (mttt) REVERT: B 138 LYS cc_start: 0.7854 (mptt) cc_final: 0.7599 (mptt) REVERT: B 139 GLU cc_start: 0.7838 (tt0) cc_final: 0.7558 (tt0) REVERT: B 166 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: C 17 THR cc_start: 0.6707 (p) cc_final: 0.6459 (m) REVERT: C 41 LYS cc_start: 0.8103 (tttp) cc_final: 0.7854 (ttpp) REVERT: C 48 GLU cc_start: 0.8131 (tt0) cc_final: 0.7899 (tt0) REVERT: D 31 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7982 (mp0) REVERT: D 42 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7761 (mtmm) REVERT: F 31 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7986 (mp0) REVERT: F 42 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7685 (mtmm) REVERT: F 61 ARG cc_start: 0.7236 (ptp-170) cc_final: 0.6967 (ptp90) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.5442 time to fit residues: 65.6175 Evaluate side-chains 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 0.0000 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116133 restraints weight = 7079.103| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.10 r_work: 0.3084 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7066 Z= 0.090 Angle : 0.495 6.076 9568 Z= 0.253 Chirality : 0.039 0.126 1054 Planarity : 0.005 0.051 1156 Dihedral : 10.128 155.143 1006 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.63 % Allowed : 15.80 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 2.08 (0.30), residues: 840 helix: 2.49 (0.28), residues: 306 sheet: 1.36 (0.36), residues: 240 loop : 0.25 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR C 96 PHE 0.015 0.001 PHE A 39 TRP 0.009 0.001 TRP E 110 HIS 0.004 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 ( 7058) covalent geometry : angle 0.49475 / 0.25 ( 9564) SS BOND : bond 0.00052 / 0.03 ( 2) SS BOND : angle 0.20647 / 0.12 ( 4) hydrogen bonds : bond 0.03601 / 2.40 ( 374) hydrogen bonds : angle 4.31154 / 3.10 ( 1038) metal coordination : bond 0.00076 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.293 Fit side-chains REVERT: A 27 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7827 (mttt) REVERT: A 139 GLU cc_start: 0.7788 (tt0) cc_final: 0.7498 (tt0) REVERT: B 27 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7933 (mttt) REVERT: B 138 LYS cc_start: 0.7802 (mptt) cc_final: 0.7536 (mptt) REVERT: B 139 GLU cc_start: 0.7815 (tt0) cc_final: 0.7557 (tt0) REVERT: B 166 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7621 (mmm) REVERT: C 41 LYS cc_start: 0.8102 (tttp) cc_final: 0.7679 (tptp) REVERT: C 48 GLU cc_start: 0.8062 (tt0) cc_final: 0.7831 (tt0) REVERT: D 31 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7952 (mp0) REVERT: D 42 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7663 (mtmm) REVERT: E 17 THR cc_start: 0.6578 (p) cc_final: 0.6265 (m) REVERT: F 31 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7941 (mp0) REVERT: F 42 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7696 (mtmm) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 0.5453 time to fit residues: 67.5666 Evaluate side-chains 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112211 restraints weight = 6999.547| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.10 r_work: 0.3078 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7066 Z= 0.115 Angle : 0.524 6.240 9568 Z= 0.268 Chirality : 0.041 0.139 1054 Planarity : 0.005 0.051 1156 Dihedral : 9.974 149.891 1006 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 16.21 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 2.00 (0.30), residues: 840 helix: 2.36 (0.27), residues: 304 sheet: 1.38 (0.35), residues: 240 loop : 0.26 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.011 0.001 TYR D 86 PHE 0.017 0.002 PHE B 46 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7058) covalent geometry : angle 0.52381 / 0.27 ( 9564) SS BOND : bond 0.00001 / 0.00 ( 2) SS BOND : angle 0.01812 / 0.01 ( 4) hydrogen bonds : bond 0.04034 / 2.70 ( 374) hydrogen bonds : angle 4.42629 / 3.18 ( 1038) metal coordination : bond 0.00160 / 0.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.168 Fit side-chains REVERT: A 27 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7909 (mttt) REVERT: A 139 GLU cc_start: 0.7827 (tt0) cc_final: 0.7541 (tt0) REVERT: B 27 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7908 (mttt) REVERT: B 138 LYS cc_start: 0.7898 (mptt) cc_final: 0.7629 (mptt) REVERT: B 139 GLU cc_start: 0.7901 (tt0) cc_final: 0.7596 (tt0) REVERT: B 166 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7789 (mmm) REVERT: C 41 LYS cc_start: 0.8163 (tttp) cc_final: 0.7888 (ttpp) REVERT: C 48 GLU cc_start: 0.8086 (tt0) cc_final: 0.7858 (tt0) REVERT: C 66 LYS cc_start: 0.6748 (tttt) cc_final: 0.6394 (tttm) REVERT: D 31 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8078 (mp0) REVERT: D 42 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7837 (mtmm) REVERT: E 17 THR cc_start: 0.6603 (p) cc_final: 0.6301 (m) REVERT: F 31 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8044 (mp0) REVERT: F 42 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7795 (mtmm) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.4699 time to fit residues: 55.8178 Evaluate side-chains 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.0050 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN E 112 GLN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112722 restraints weight = 7002.831| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.10 r_work: 0.3088 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7066 Z= 0.112 Angle : 0.524 6.233 9568 Z= 0.267 Chirality : 0.041 0.136 1054 Planarity : 0.005 0.051 1156 Dihedral : 9.906 147.001 1006 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.23 % Allowed : 16.49 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 2.04 (0.30), residues: 840 helix: 2.35 (0.28), residues: 304 sheet: 1.43 (0.36), residues: 240 loop : 0.28 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.011 0.001 TYR D 91 PHE 0.016 0.002 PHE A 46 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7058) covalent geometry : angle 0.52366 / 0.27 ( 9564) SS BOND : bond 0.00024 / 0.01 ( 2) SS BOND : angle 0.04260 / 0.02 ( 4) hydrogen bonds : bond 0.03981 / 2.67 ( 374) hydrogen bonds : angle 4.41076 / 3.18 ( 1038) metal coordination : bond 0.00161 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.38 seconds wall clock time: 46 minutes 40.96 seconds (2800.96 seconds total)