Starting phenix.real_space_refine on Wed Mar 12 04:42:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t03_40933/03_2025/8t03_40933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/03_2025/8t03_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_40933/03_2025/8t03_40933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/03_2025/8t03_40933.map" model { file = "/net/cci-nas-00/data/ceres_data/8t03_40933/03_2025/8t03_40933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/03_2025/8t03_40933.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: E, F, B Time building chain proxies: 5.12, per 1000 atoms: 0.74 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: 1.67 Conformation dependent library (CDL) restraints added in 954.7 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: 0.89 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: 2.12 Time building geometry restraints manager: 1.96 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: 4118 35.87 - 71.74: 116 71.74 - 107.61: 4 107.61 - 143.48: 2 143.48 - 179.35: 4 Dihedral angle restraints: 4244 sinusoidal: 1782 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 4241 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.014 0.050 7058 Z= 0.887 Angle : 1.758 11.254 9564 Z= 1.287 Chirality : 0.227 4.848 1054 Planarity : 0.004 0.051 1156 Dihedral : 17.024 179.354 2666 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP E 110 HIS 0.008 0.002 HIS B 110 PHE 0.022 0.003 PHE A 46 TYR 0.027 0.003 TYR F 71 ARG 0.003 0.001 ARG B 168 *********************** 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 : 0.719 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: 0.6456 (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: 0.7319 (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: 0.7029 (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: 1.1827 time to fit residues: 166.7601 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 : 0.752 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3846 r_free = 0.3846 target = 0.162287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117157 restraints weight = 6893.788| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.41 r_work: 0.3100 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7058 Z= 0.186 Angle : 0.587 6.356 9564 Z= 0.305 Chirality : 0.043 0.147 1054 Planarity : 0.004 0.034 1156 Dihedral : 13.858 162.556 1144 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 8.86 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.30), residues: 840 helix: 1.60 (0.28), residues: 304 sheet: 0.64 (0.35), residues: 230 loop : -0.17 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 110 HIS 0.003 0.001 HIS A 110 PHE 0.018 0.002 PHE A 39 TYR 0.012 0.001 TYR F 91 ARG 0.002 0.000 ARG C 68 *********************** 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 : 0.673 Fit side-chains REVERT: A 27 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7700 (mttt) REVERT: A 139 GLU cc_start: 0.7852 (tt0) cc_final: 0.7604 (tt0) REVERT: B 27 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7761 (mttt) REVERT: B 139 GLU cc_start: 0.7839 (tt0) cc_final: 0.7592 (tt0) REVERT: D 31 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8040 (mp0) REVERT: D 45 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8012 (mtp180) REVERT: E 41 LYS cc_start: 0.7883 (tttt) cc_final: 0.7641 (ttpp) REVERT: F 31 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8012 (mp0) REVERT: F 42 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7832 (mtmm) REVERT: F 67 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.6993 (p) outliers start: 19 outliers final: 5 residues processed: 125 average time/residue: 1.3951 time to fit residues: 183.3038 Evaluate side-chains 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 61 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3845 r_free = 0.3845 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113903 restraints weight = 7029.169| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.08 r_work: 0.3099 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7058 Z= 0.151 Angle : 0.530 6.215 9564 Z= 0.274 Chirality : 0.041 0.144 1054 Planarity : 0.004 0.033 1156 Dihedral : 12.712 162.830 1136 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.72 % Allowed : 12.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.30), residues: 840 helix: 2.05 (0.28), residues: 306 sheet: 0.75 (0.34), residues: 240 loop : 0.08 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.001 PHE A 46 TYR 0.011 0.001 TYR D 91 ARG 0.001 0.000 ARG A 107 *********************** 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 130 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.757 Fit side-chains REVERT: A 27 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7941 (mttt) REVERT: A 139 GLU cc_start: 0.7890 (tt0) cc_final: 0.7614 (tt0) REVERT: B 27 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7944 (mttt) REVERT: B 139 GLU cc_start: 0.7885 (tt0) cc_final: 0.7606 (tt0) REVERT: C 41 LYS cc_start: 0.8174 (tttp) cc_final: 0.7794 (tptm) REVERT: D 31 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8061 (mp0) REVERT: F 5 THR cc_start: 0.7730 (m) cc_final: 0.7463 (p) REVERT: F 31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8012 (mp0) REVERT: F 42 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7859 (mtmm) outliers start: 20 outliers final: 7 residues processed: 114 average time/residue: 1.3852 time to fit residues: 165.6448 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 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 112 GLN Chi-restraints excluded: chain F residue 45 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3797 r_free = 0.3797 target = 0.158063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113012 restraints weight = 7047.831| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.95 r_work: 0.3010 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7058 Z= 0.273 Angle : 0.588 6.555 9564 Z= 0.302 Chirality : 0.044 0.149 1054 Planarity : 0.005 0.038 1156 Dihedral : 12.875 160.272 1136 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.13 % Allowed : 12.94 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.30), residues: 840 helix: 1.98 (0.28), residues: 304 sheet: 0.91 (0.35), residues: 240 loop : -0.00 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 110 HIS 0.004 0.001 HIS D 38 PHE 0.018 0.002 PHE B 69 TYR 0.014 0.002 TYR D 86 ARG 0.003 0.000 ARG A 29 *********************** 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 131 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.847 Fit side-chains REVERT: A 27 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7872 (mttt) REVERT: A 139 GLU cc_start: 0.8010 (tt0) cc_final: 0.7724 (tt0) REVERT: A 166 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: A 168 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: B 27 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7874 (mttt) REVERT: B 139 GLU cc_start: 0.8003 (tt0) cc_final: 0.7714 (tt0) REVERT: B 166 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: C 41 LYS cc_start: 0.8243 (tttp) cc_final: 0.7909 (tptp) REVERT: D 31 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8261 (mp0) REVERT: D 42 LYS cc_start: 0.8523 (mtpp) cc_final: 0.7973 (mtpt) REVERT: D 61 ARG cc_start: 0.7160 (ptt90) cc_final: 0.6845 (ptp90) REVERT: F 5 THR cc_start: 0.7771 (m) cc_final: 0.7515 (p) REVERT: F 31 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8185 (mp0) REVERT: F 42 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7985 (mtmm) outliers start: 23 outliers final: 8 residues processed: 112 average time/residue: 1.8642 time to fit residues: 219.8936 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 168 ARG 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 68 ARG Chi-restraints excluded: chain E residue 70 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 63 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3789 r_free = 0.3789 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112530 restraints weight = 6995.209| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.94 r_work: 0.3008 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7058 Z= 0.270 Angle : 0.579 6.562 9564 Z= 0.299 Chirality : 0.044 0.145 1054 Planarity : 0.005 0.044 1156 Dihedral : 12.414 156.793 1136 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.86 % Allowed : 13.62 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.30), residues: 840 helix: 1.93 (0.28), residues: 304 sheet: 0.96 (0.35), residues: 240 loop : -0.03 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 110 HIS 0.004 0.001 HIS F 38 PHE 0.018 0.002 PHE A 69 TYR 0.014 0.002 TYR F 86 ARG 0.003 0.000 ARG B 107 *********************** 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 132 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.758 Fit side-chains REVERT: A 27 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7870 (mttt) REVERT: A 63 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: A 139 GLU cc_start: 0.7979 (tt0) cc_final: 0.7710 (tt0) REVERT: A 166 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7902 (mmm) REVERT: A 168 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7531 (ttt180) REVERT: B 27 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7872 (mttt) REVERT: B 139 GLU cc_start: 0.7970 (tt0) cc_final: 0.7690 (tt0) REVERT: C 41 LYS cc_start: 0.8310 (tttp) cc_final: 0.7942 (tptp) REVERT: D 31 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8259 (mp0) REVERT: D 42 LYS cc_start: 0.8489 (mtpp) cc_final: 0.7962 (mtmm) REVERT: F 31 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8201 (mp0) REVERT: F 42 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7978 (mtmm) outliers start: 21 outliers final: 9 residues processed: 119 average time/residue: 1.6320 time to fit residues: 203.6770 Evaluate side-chains 118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 168 ARG Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 134 LEU 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 Chi-restraints excluded: chain F residue 45 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 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 = 0.3827 r_free = 0.3827 target = 0.160520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112133 restraints weight = 7029.351| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.09 r_work: 0.3074 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7058 Z= 0.159 Angle : 0.518 6.236 9564 Z= 0.268 Chirality : 0.041 0.142 1054 Planarity : 0.005 0.047 1156 Dihedral : 11.543 148.494 1136 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.00 % Allowed : 13.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.30), residues: 840 helix: 2.20 (0.28), residues: 306 sheet: 1.15 (0.35), residues: 240 loop : 0.02 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.004 0.001 HIS E 52 PHE 0.016 0.001 PHE A 39 TYR 0.010 0.001 TYR C 96 ARG 0.001 0.000 ARG A 29 *********************** 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 132 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.843 Fit side-chains REVERT: A 27 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7882 (mttt) REVERT: A 139 GLU cc_start: 0.7874 (tt0) cc_final: 0.7558 (tt0) REVERT: A 166 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7746 (mmm) REVERT: B 27 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7890 (mttt) REVERT: B 139 GLU cc_start: 0.7857 (tt0) cc_final: 0.7544 (tt0) REVERT: C 41 LYS cc_start: 0.8209 (tttp) cc_final: 0.7643 (tptp) REVERT: D 31 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8118 (mp0) REVERT: D 42 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7846 (mtmm) REVERT: D 61 ARG cc_start: 0.7474 (ptp90) cc_final: 0.7268 (ptp90) REVERT: F 31 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8075 (mp0) REVERT: F 42 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7855 (mtmm) REVERT: F 69 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7853 (mtp-110) outliers start: 22 outliers final: 8 residues processed: 117 average time/residue: 1.8878 time to fit residues: 230.4517 Evaluate side-chains 112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 70 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN 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 = 0.3832 r_free = 0.3832 target = 0.160859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112511 restraints weight = 6953.104| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.10 r_work: 0.3080 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7058 Z= 0.157 Angle : 0.516 6.249 9564 Z= 0.266 Chirality : 0.041 0.140 1054 Planarity : 0.005 0.051 1156 Dihedral : 11.260 143.276 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.59 % Allowed : 15.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.30), residues: 840 helix: 2.33 (0.28), residues: 304 sheet: 1.23 (0.35), residues: 240 loop : 0.04 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE A 39 TYR 0.010 0.001 TYR F 91 ARG 0.002 0.000 ARG B 29 *********************** 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 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.834 Fit side-chains REVERT: A 27 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7983 (mttt) REVERT: A 139 GLU cc_start: 0.7897 (tt0) cc_final: 0.7585 (tt0) REVERT: B 27 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7984 (mttt) REVERT: B 139 GLU cc_start: 0.7874 (tt0) cc_final: 0.7562 (tt0) REVERT: B 166 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7756 (mmm) REVERT: C 17 THR cc_start: 0.6628 (p) cc_final: 0.6389 (m) REVERT: C 41 LYS cc_start: 0.8167 (tttp) cc_final: 0.7761 (tptp) REVERT: D 31 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8070 (mp0) REVERT: D 42 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7826 (mtpt) REVERT: F 31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8045 (mp0) REVERT: F 42 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7835 (mtmm) outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 1.4703 time to fit residues: 172.5747 Evaluate side-chains 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 13 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3861 r_free = 0.3861 target = 0.163484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115738 restraints weight = 7065.638| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.10 r_work: 0.3086 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7058 Z= 0.120 Angle : 0.491 6.075 9564 Z= 0.252 Chirality : 0.040 0.148 1054 Planarity : 0.004 0.051 1156 Dihedral : 10.641 133.641 1136 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.36 % Allowed : 16.49 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.30), residues: 840 helix: 2.51 (0.28), residues: 306 sheet: 1.37 (0.35), residues: 240 loop : 0.21 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.004 0.001 HIS E 52 PHE 0.015 0.001 PHE A 39 TYR 0.011 0.001 TYR C 96 ARG 0.001 0.000 ARG C 68 *********************** 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 122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.856 Fit side-chains REVERT: A 27 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7897 (mttt) REVERT: A 138 LYS cc_start: 0.7807 (mptt) cc_final: 0.7555 (mptt) REVERT: A 139 GLU cc_start: 0.7811 (tt0) cc_final: 0.7503 (tt0) REVERT: B 27 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7903 (mttt) REVERT: B 138 LYS cc_start: 0.7800 (mptt) cc_final: 0.7548 (mptt) REVERT: B 139 GLU cc_start: 0.7797 (tt0) cc_final: 0.7506 (tt0) REVERT: C 41 LYS cc_start: 0.8093 (tttp) cc_final: 0.7450 (tptp) REVERT: D 31 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7933 (mp0) REVERT: D 42 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7634 (mtmm) REVERT: D 61 ARG cc_start: 0.7335 (ptp90) cc_final: 0.7061 (ptp90) REVERT: E 17 THR cc_start: 0.6595 (p) cc_final: 0.6294 (m) REVERT: F 31 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7924 (mp0) REVERT: F 42 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7662 (mtmm) REVERT: F 61 ARG cc_start: 0.7219 (ptp-170) cc_final: 0.6991 (ptp90) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 1.2942 time to fit residues: 156.5657 Evaluate side-chains 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 41 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN 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 = 0.3833 r_free = 0.3833 target = 0.160970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112583 restraints weight = 7034.713| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.10 r_work: 0.3082 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7058 Z= 0.160 Angle : 0.515 6.245 9564 Z= 0.264 Chirality : 0.041 0.142 1054 Planarity : 0.005 0.051 1156 Dihedral : 10.609 134.061 1136 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 15.67 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 840 helix: 2.39 (0.27), residues: 304 sheet: 1.39 (0.35), residues: 240 loop : 0.26 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.017 0.001 PHE A 46 TYR 0.011 0.001 TYR F 86 ARG 0.001 0.000 ARG D 45 *********************** 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 127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.787 Fit side-chains REVERT: A 27 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7930 (mttt) REVERT: A 138 LYS cc_start: 0.7937 (mptt) cc_final: 0.7669 (mptt) REVERT: A 139 GLU cc_start: 0.7887 (tt0) cc_final: 0.7600 (tt0) REVERT: B 27 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7931 (mttt) REVERT: B 138 LYS cc_start: 0.7933 (mptt) cc_final: 0.7667 (mptt) REVERT: B 139 GLU cc_start: 0.7887 (tt0) cc_final: 0.7603 (tt0) REVERT: B 152 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: B 166 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: C 41 LYS cc_start: 0.8192 (tttp) cc_final: 0.7567 (tptp) REVERT: D 31 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8089 (mp0) REVERT: D 42 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7807 (mtmm) REVERT: D 61 ARG cc_start: 0.7446 (ptp90) cc_final: 0.7128 (ptp90) REVERT: E 17 THR cc_start: 0.6570 (p) cc_final: 0.6277 (m) REVERT: F 31 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8075 (mp0) REVERT: F 42 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7812 (mtmm) outliers start: 18 outliers final: 8 residues processed: 116 average time/residue: 1.2983 time to fit residues: 158.2675 Evaluate side-chains 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 152 GLN 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 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN E 112 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 = 0.3830 r_free = 0.3830 target = 0.160680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112209 restraints weight = 7056.773| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.10 r_work: 0.3083 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.166 Angle : 0.520 6.254 9564 Z= 0.268 Chirality : 0.041 0.141 1054 Planarity : 0.005 0.051 1156 Dihedral : 10.854 135.300 1136 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 16.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 840 helix: 2.33 (0.28), residues: 304 sheet: 1.43 (0.35), residues: 240 loop : 0.27 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 PHE 0.016 0.002 PHE A 46 TYR 0.011 0.001 TYR D 86 ARG 0.001 0.000 ARG C 68 ********************** 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 : 0.752 Fit side-chains REVERT: A 27 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7732 (mttt) REVERT: A 138 LYS cc_start: 0.7847 (mptt) cc_final: 0.7567 (mptt) REVERT: A 139 GLU cc_start: 0.7826 (tt0) cc_final: 0.7511 (tt0) REVERT: B 27 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7726 (mttt) REVERT: B 138 LYS cc_start: 0.7845 (mptt) cc_final: 0.7568 (mptt) REVERT: B 139 GLU cc_start: 0.7827 (tt0) cc_final: 0.7517 (tt0) REVERT: B 152 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: B 166 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: C 41 LYS cc_start: 0.8097 (tttp) cc_final: 0.7457 (tptp) REVERT: D 31 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7997 (mp0) REVERT: D 42 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7727 (mtmm) REVERT: D 61 ARG cc_start: 0.7452 (ptp90) cc_final: 0.7132 (ptp90) REVERT: E 17 THR cc_start: 0.6575 (p) cc_final: 0.6280 (m) REVERT: F 31 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7987 (mp0) REVERT: F 42 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7741 (mtmm) outliers start: 11 outliers final: 9 residues processed: 112 average time/residue: 1.2939 time to fit residues: 152.1531 Evaluate side-chains 117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 152 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3804 r_free = 0.3804 target = 0.158427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109604 restraints weight = 6995.470| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.10 r_work: 0.3042 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7058 Z= 0.232 Angle : 0.563 6.432 9564 Z= 0.289 Chirality : 0.043 0.148 1054 Planarity : 0.005 0.050 1156 Dihedral : 11.200 139.071 1136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.04 % Allowed : 16.08 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.30), residues: 840 helix: 2.12 (0.28), residues: 304 sheet: 1.41 (0.35), residues: 240 loop : 0.22 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.004 0.001 HIS F 38 PHE 0.018 0.002 PHE A 46 TYR 0.014 0.002 TYR D 91 ARG 0.002 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6573.25 seconds wall clock time: 117 minutes 3.72 seconds (7023.72 seconds total)