Starting phenix.real_space_refine on Mon Jun 9 03:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubd_42083/06_2025/8ubd_42083.cif" } resolution = 3.05 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= -0.000 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 36 5.16 5 C 6058 2.51 5 N 1869 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10368 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2628 Classifications: {'RNA': 123} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 52, 'rna3p_pyr': 47} Link IDs: {'rna2p': 24, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 7.67, per 1000 atoms: 0.74 Number of scatterers: 10368 At special positions: 0 Unit cell: (82, 98, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 149 15.00 O 2256 8.00 N 1869 7.00 C 6058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 962.5 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 2 sheets defined 76.1% alpha, 2.0% beta 45 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.591A pdb=" N ILE A 146 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.606A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.993A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.566A pdb=" N LYS A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 310 removed outlier: 3.903A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.668A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 62 removed outlier: 4.182A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.501A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.714A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 64 through 87 Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.769A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.523A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.716A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.671A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 32 removed outlier: 4.488A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.574A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.385A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.698A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1320 1.31 - 1.44: 3777 1.44 - 1.56: 5444 1.56 - 1.69: 300 1.69 - 1.82: 60 Bond restraints: 10901 Sorted by residual: bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.530 1.637 -0.107 1.69e-02 3.50e+03 4.01e+01 bond pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " ideal model delta sigma weight residual 1.528 1.621 -0.092 1.56e-02 4.11e+03 3.49e+01 bond pdb=" CG MET C 77 " pdb=" SD MET C 77 " ideal model delta sigma weight residual 1.803 1.685 0.118 2.50e-02 1.60e+03 2.22e+01 bond pdb=" O3' G I 53 " pdb=" P U I 54 " ideal model delta sigma weight residual 1.607 1.676 -0.069 1.50e-02 4.44e+03 2.14e+01 bond pdb=" CA ARG B 111 " pdb=" CB ARG B 111 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.55e-02 4.16e+03 2.01e+01 ... (remaining 10896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 15215 5.06 - 10.13: 229 10.13 - 15.19: 6 15.19 - 20.25: 2 20.25 - 25.32: 1 Bond angle restraints: 15453 Sorted by residual: angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 103.76 16.44 1.50e+00 4.44e-01 1.20e+02 angle pdb=" OP2 A I 88 " pdb=" P A I 88 " pdb=" O5' A I 88 " ideal model delta sigma weight residual 108.00 82.68 25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C3' G I 122 " pdb=" O3' G I 122 " pdb=" P A I 123 " ideal model delta sigma weight residual 120.20 108.00 12.20 1.50e+00 4.44e-01 6.61e+01 angle pdb=" C3' G I 105 " pdb=" O3' G I 105 " pdb=" P U I 106 " ideal model delta sigma weight residual 120.20 108.49 11.71 1.50e+00 4.44e-01 6.10e+01 angle pdb=" C4' A I 13 " pdb=" C3' A I 13 " pdb=" O3' A I 13 " ideal model delta sigma weight residual 113.00 102.41 10.59 1.50e+00 4.44e-01 4.98e+01 ... (remaining 15448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5908 35.76 - 71.51: 776 71.51 - 107.27: 74 107.27 - 143.03: 3 143.03 - 178.79: 3 Dihedral angle restraints: 6764 sinusoidal: 4175 harmonic: 2589 Sorted by residual: dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 60.87 171.13 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C5' C I 91 " pdb=" C4' C I 91 " pdb=" C3' C I 91 " pdb=" O3' C I 91 " ideal model delta sinusoidal sigma weight residual 147.00 99.97 47.03 1 8.00e+00 1.56e-02 4.78e+01 ... (remaining 6761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1603 0.161 - 0.321: 195 0.321 - 0.482: 28 0.482 - 0.642: 7 0.642 - 0.803: 3 Chirality restraints: 1836 Sorted by residual: chirality pdb=" P C I 113 " pdb=" OP1 C I 113 " pdb=" OP2 C I 113 " pdb=" O5' C I 113 " both_signs ideal model delta sigma weight residual True 2.41 -1.61 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.07 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P A I 88 " pdb=" OP1 A I 88 " pdb=" OP2 A I 88 " pdb=" O5' A I 88 " both_signs ideal model delta sigma weight residual True 2.41 -3.07 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1833 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.099 2.00e-02 2.50e+03 5.08e-02 5.17e+01 pdb=" CG TYR C 28 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.063 2.00e-02 2.50e+03 3.28e-02 2.43e+01 pdb=" N1 U I 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.022 2.00e-02 2.50e+03 pdb=" N3 U I 7 " -0.037 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.023 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " -0.017 2.00e-02 2.50e+03 2.92e-02 1.70e+01 pdb=" CG TYR B 11 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " 0.032 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 662 2.69 - 3.24: 10846 3.24 - 3.79: 22486 3.79 - 4.35: 28956 4.35 - 4.90: 40487 Nonbonded interactions: 103437 Sorted by model distance: nonbonded pdb=" OP2 A I 88 " pdb=" C5' A I 88 " model vdw 2.132 2.752 nonbonded pdb=" O SER E 33 " pdb=" O2' C I 23 " model vdw 2.196 3.040 nonbonded pdb=" C4' G I 92 " pdb=" OP1 G I 93 " model vdw 2.205 3.470 nonbonded pdb=" NE2 HIS A 202 " pdb=" O3' G I 129 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.219 3.120 ... (remaining 103432 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 1.820 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.250 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 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 : 0.012 0.118 10901 Z= 0.720 Angle : 1.616 25.318 15453 Z= 0.978 Chirality : 0.116 0.803 1836 Planarity : 0.011 0.108 1396 Dihedral : 25.589 178.787 5094 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 43.56 Ramachandran Plot: Outliers : 3.77 % Allowed : 10.16 % Favored : 86.07 % Rotamer: Outliers : 20.43 % Allowed : 14.25 % Favored : 65.32 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.23), residues: 876 helix: -1.87 (0.16), residues: 667 sheet: -4.97 (0.82), residues: 24 loop : -4.18 (0.35), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.009 TRP C 116 HIS 0.029 0.005 HIS A 306 PHE 0.048 0.008 PHE A 231 TYR 0.099 0.011 TYR C 28 ARG 0.028 0.003 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.19844 ( 596) hydrogen bonds : angle 9.09892 ( 1608) covalent geometry : bond 0.01226 (10901) covalent geometry : angle 1.61587 (15453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 234 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.4603 (ptm) REVERT: A 31 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7200 (ptm-80) REVERT: A 75 LEU cc_start: 0.4063 (OUTLIER) cc_final: 0.3853 (tt) REVERT: A 107 TYR cc_start: 0.8645 (m-80) cc_final: 0.8260 (m-80) REVERT: A 123 GLN cc_start: 0.6296 (tt0) cc_final: 0.5639 (tt0) REVERT: A 127 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.3815 (mtt180) REVERT: A 165 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6939 (mtp180) REVERT: A 172 LEU cc_start: 0.7708 (tp) cc_final: 0.7353 (tt) REVERT: A 226 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 227 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.7001 (mp) REVERT: A 228 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7828 (ttm110) REVERT: A 245 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6945 (tmtt) REVERT: A 269 HIS cc_start: 0.6950 (p-80) cc_final: 0.6592 (p90) REVERT: A 296 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3630 (mt) REVERT: B 66 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 89 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6555 (mt0) REVERT: C 13 GLN cc_start: 0.5585 (tm-30) cc_final: 0.5187 (pm20) REVERT: C 14 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5802 (mmm) REVERT: C 18 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7268 (pt0) REVERT: C 21 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6584 (tt0) REVERT: C 38 HIS cc_start: 0.7755 (m-70) cc_final: 0.7478 (m-70) REVERT: C 47 LYS cc_start: 0.7184 (mttm) cc_final: 0.6858 (ttpp) REVERT: C 54 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: C 72 ASP cc_start: 0.7333 (t70) cc_final: 0.6916 (t0) REVERT: D 19 ARG cc_start: 0.6980 (mmt-90) cc_final: 0.6309 (mmt-90) REVERT: D 26 TYR cc_start: 0.6561 (t80) cc_final: 0.5839 (t80) REVERT: D 43 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6212 (tt0) REVERT: D 52 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: D 62 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7190 (p) REVERT: D 89 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7352 (tp40) REVERT: D 95 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6342 (p) REVERT: D 103 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (mm-40) REVERT: D 108 GLU cc_start: 0.6985 (tt0) cc_final: 0.6674 (tp30) REVERT: D 111 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7402 (mtt180) REVERT: E 52 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: E 54 GLU cc_start: 0.7222 (tt0) cc_final: 0.6884 (tm-30) REVERT: E 77 MET cc_start: 0.7490 (tpt) cc_final: 0.7167 (tpt) REVERT: E 119 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6543 (ppt170) REVERT: F 18 GLU cc_start: 0.7525 (mp0) cc_final: 0.7215 (pp20) REVERT: F 19 ARG cc_start: 0.6241 (tpp80) cc_final: 0.5895 (mmm160) REVERT: F 25 SER cc_start: 0.8163 (t) cc_final: 0.7831 (p) REVERT: F 26 TYR cc_start: 0.6575 (t80) cc_final: 0.6118 (t80) REVERT: F 43 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: F 47 LYS cc_start: 0.6543 (mttm) cc_final: 0.6174 (ttpt) REVERT: F 54 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6307 (tp30) REVERT: F 77 MET cc_start: 0.7335 (tpt) cc_final: 0.6776 (tpt) REVERT: F 85 LEU cc_start: 0.7450 (mt) cc_final: 0.7126 (mp) REVERT: F 90 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6906 (mmtp) REVERT: F 98 GLN cc_start: 0.7752 (mt0) cc_final: 0.7461 (mt0) outliers start: 152 outliers final: 33 residues processed: 337 average time/residue: 0.3222 time to fit residues: 137.3578 Evaluate side-chains 245 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 ARG Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 111 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 116 HIS A 306 HIS B 64 GLN C 121 ASN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.236527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178743 restraints weight = 12384.743| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.68 r_work: 0.3862 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10901 Z= 0.207 Angle : 0.754 8.514 15453 Z= 0.387 Chirality : 0.042 0.184 1836 Planarity : 0.006 0.057 1396 Dihedral : 24.245 179.933 3494 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.31 % Favored : 91.89 % Rotamer: Outliers : 6.99 % Allowed : 19.35 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.28), residues: 876 helix: -0.19 (0.19), residues: 663 sheet: -4.01 (0.81), residues: 26 loop : -3.04 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 116 HIS 0.012 0.002 HIS A 116 PHE 0.019 0.003 PHE F 80 TYR 0.024 0.002 TYR C 28 ARG 0.005 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 596) hydrogen bonds : angle 4.93705 ( 1608) covalent geometry : bond 0.00464 (10901) covalent geometry : angle 0.75354 (15453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7415 (mmt) cc_final: 0.6007 (ptm) REVERT: A 105 TYR cc_start: 0.7996 (m-10) cc_final: 0.7650 (m-80) REVERT: A 193 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 264 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7489 (mmm-85) REVERT: C 98 GLN cc_start: 0.7603 (mt0) cc_final: 0.7288 (mt0) REVERT: D 52 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: F 43 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7323 (mp0) outliers start: 52 outliers final: 21 residues processed: 256 average time/residue: 0.2782 time to fit residues: 94.3279 Evaluate side-chains 203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 286 ASN A 290 HIS ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN F 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.238722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181645 restraints weight = 12607.530| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.63 r_work: 0.3888 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10901 Z= 0.192 Angle : 0.688 9.140 15453 Z= 0.350 Chirality : 0.039 0.187 1836 Planarity : 0.005 0.047 1396 Dihedral : 23.700 177.315 3396 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.42 % Favored : 92.12 % Rotamer: Outliers : 4.97 % Allowed : 20.83 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.28), residues: 876 helix: 0.10 (0.19), residues: 660 sheet: -2.87 (0.95), residues: 24 loop : -2.77 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 116 HIS 0.013 0.001 HIS A 269 PHE 0.019 0.002 PHE D 80 TYR 0.020 0.002 TYR C 28 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.05352 ( 596) hydrogen bonds : angle 4.62728 ( 1608) covalent geometry : bond 0.00439 (10901) covalent geometry : angle 0.68794 (15453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7288 (mmt) cc_final: 0.6051 (ptm) REVERT: A 184 LEU cc_start: 0.8051 (tp) cc_final: 0.7749 (tp) REVERT: A 193 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 250 GLN cc_start: 0.6536 (pt0) cc_final: 0.6198 (pm20) REVERT: B 77 MET cc_start: 0.7753 (tpt) cc_final: 0.7340 (tpt) REVERT: C 14 MET cc_start: 0.6518 (tpt) cc_final: 0.6187 (mmm) REVERT: D 52 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: F 43 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7232 (mt-10) outliers start: 37 outliers final: 22 residues processed: 219 average time/residue: 0.2721 time to fit residues: 79.9494 Evaluate side-chains 201 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.236009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179483 restraints weight = 12374.986| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.70 r_work: 0.3864 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10901 Z= 0.201 Angle : 0.680 8.072 15453 Z= 0.345 Chirality : 0.038 0.186 1836 Planarity : 0.005 0.034 1396 Dihedral : 23.428 176.442 3386 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.53 % Favored : 92.01 % Rotamer: Outliers : 4.17 % Allowed : 22.31 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.28), residues: 876 helix: 0.22 (0.19), residues: 659 sheet: -1.66 (1.12), residues: 24 loop : -2.75 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 116 HIS 0.006 0.001 HIS A 269 PHE 0.020 0.002 PHE D 80 TYR 0.028 0.003 TYR A 58 ARG 0.005 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 596) hydrogen bonds : angle 4.64646 ( 1608) covalent geometry : bond 0.00466 (10901) covalent geometry : angle 0.68043 (15453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7276 (mmt) cc_final: 0.6040 (ptm) REVERT: A 105 TYR cc_start: 0.8157 (m-80) cc_final: 0.7535 (m-80) REVERT: A 128 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7658 (ttp-170) REVERT: A 136 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5921 (tptm) REVERT: A 184 LEU cc_start: 0.8045 (tp) cc_final: 0.7741 (tp) REVERT: A 250 GLN cc_start: 0.6631 (pt0) cc_final: 0.6093 (pm20) REVERT: A 290 HIS cc_start: 0.0958 (OUTLIER) cc_final: 0.0268 (t-90) REVERT: B 77 MET cc_start: 0.7936 (tpt) cc_final: 0.7193 (tpt) REVERT: D 52 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: E 16 ILE cc_start: 0.8103 (mt) cc_final: 0.7858 (tt) outliers start: 31 outliers final: 20 residues processed: 204 average time/residue: 0.2550 time to fit residues: 70.4334 Evaluate side-chains 197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.236607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178805 restraints weight = 12618.056| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.70 r_work: 0.3828 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10901 Z= 0.199 Angle : 0.666 7.991 15453 Z= 0.339 Chirality : 0.038 0.196 1836 Planarity : 0.005 0.033 1396 Dihedral : 23.314 176.143 3385 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.08 % Favored : 92.58 % Rotamer: Outliers : 3.76 % Allowed : 22.98 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.28), residues: 876 helix: 0.34 (0.19), residues: 662 sheet: -1.06 (1.17), residues: 24 loop : -2.72 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 116 HIS 0.022 0.002 HIS A 121 PHE 0.031 0.003 PHE A 260 TYR 0.025 0.003 TYR C 28 ARG 0.006 0.001 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 596) hydrogen bonds : angle 4.60527 ( 1608) covalent geometry : bond 0.00463 (10901) covalent geometry : angle 0.66607 (15453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7314 (mmt) cc_final: 0.6013 (ptm) REVERT: A 83 ASP cc_start: 0.7967 (m-30) cc_final: 0.7766 (m-30) REVERT: A 128 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7565 (ttp-170) REVERT: A 136 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6123 (tptm) REVERT: A 184 LEU cc_start: 0.8045 (tp) cc_final: 0.7752 (tp) REVERT: A 193 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 250 GLN cc_start: 0.6759 (pt0) cc_final: 0.6285 (pm20) REVERT: A 290 HIS cc_start: 0.1197 (OUTLIER) cc_final: 0.0453 (t-90) REVERT: C 28 TYR cc_start: 0.8435 (t80) cc_final: 0.8086 (t80) REVERT: D 52 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: F 43 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7030 (mp0) outliers start: 28 outliers final: 19 residues processed: 200 average time/residue: 0.2499 time to fit residues: 67.2508 Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.0040 chunk 81 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.239101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.182593 restraints weight = 12690.393| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.62 r_work: 0.3891 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10901 Z= 0.169 Angle : 0.644 9.454 15453 Z= 0.326 Chirality : 0.036 0.198 1836 Planarity : 0.005 0.033 1396 Dihedral : 23.136 175.816 3383 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 4.03 % Allowed : 23.66 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.28), residues: 876 helix: 0.45 (0.20), residues: 662 sheet: -1.13 (1.08), residues: 24 loop : -2.50 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 116 HIS 0.016 0.001 HIS A 121 PHE 0.032 0.003 PHE A 260 TYR 0.023 0.002 TYR A 58 ARG 0.007 0.001 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 596) hydrogen bonds : angle 4.50870 ( 1608) covalent geometry : bond 0.00388 (10901) covalent geometry : angle 0.64405 (15453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7241 (mmt) cc_final: 0.5858 (ptm) REVERT: A 83 ASP cc_start: 0.8008 (m-30) cc_final: 0.7712 (m-30) REVERT: A 105 TYR cc_start: 0.8140 (m-80) cc_final: 0.7845 (m-80) REVERT: A 136 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6048 (tptm) REVERT: A 193 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 250 GLN cc_start: 0.6523 (pt0) cc_final: 0.6028 (pm20) REVERT: A 290 HIS cc_start: 0.0931 (OUTLIER) cc_final: 0.0111 (t-90) REVERT: B 11 TYR cc_start: 0.6911 (t80) cc_final: 0.6656 (t80) REVERT: C 28 TYR cc_start: 0.8446 (t80) cc_final: 0.8029 (t80) REVERT: D 52 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: F 43 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7128 (mp0) outliers start: 30 outliers final: 20 residues processed: 191 average time/residue: 0.2791 time to fit residues: 73.4438 Evaluate side-chains 185 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 96 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.236466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180002 restraints weight = 12730.543| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.77 r_work: 0.3808 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10901 Z= 0.200 Angle : 0.666 8.743 15453 Z= 0.335 Chirality : 0.037 0.195 1836 Planarity : 0.005 0.034 1396 Dihedral : 23.085 175.309 3381 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.76 % Favored : 92.01 % Rotamer: Outliers : 4.03 % Allowed : 23.52 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 876 helix: 0.42 (0.20), residues: 661 sheet: -1.40 (1.01), residues: 24 loop : -2.49 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.014 0.001 HIS A 121 PHE 0.021 0.002 PHE B 80 TYR 0.030 0.003 TYR A 58 ARG 0.007 0.001 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 596) hydrogen bonds : angle 4.62259 ( 1608) covalent geometry : bond 0.00467 (10901) covalent geometry : angle 0.66625 (15453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7245 (mmt) cc_final: 0.5793 (ptm) REVERT: A 83 ASP cc_start: 0.8087 (m-30) cc_final: 0.7813 (m-30) REVERT: A 105 TYR cc_start: 0.8220 (m-80) cc_final: 0.7980 (m-80) REVERT: A 193 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 290 HIS cc_start: 0.0850 (OUTLIER) cc_final: 0.0149 (t-90) REVERT: C 28 TYR cc_start: 0.8491 (t80) cc_final: 0.7905 (t80) REVERT: D 52 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: F 43 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7096 (mp0) outliers start: 30 outliers final: 23 residues processed: 189 average time/residue: 0.2550 time to fit residues: 64.9304 Evaluate side-chains 182 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.238684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180666 restraints weight = 12716.724| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.66 r_work: 0.3875 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10901 Z= 0.182 Angle : 0.657 7.720 15453 Z= 0.330 Chirality : 0.036 0.197 1836 Planarity : 0.005 0.034 1396 Dihedral : 23.040 175.356 3381 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.35 % Rotamer: Outliers : 4.44 % Allowed : 23.12 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 876 helix: 0.42 (0.20), residues: 661 sheet: -1.74 (0.94), residues: 24 loop : -2.45 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 116 HIS 0.013 0.001 HIS A 121 PHE 0.027 0.003 PHE A 260 TYR 0.026 0.002 TYR A 58 ARG 0.007 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 596) hydrogen bonds : angle 4.61075 ( 1608) covalent geometry : bond 0.00426 (10901) covalent geometry : angle 0.65706 (15453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7270 (mmt) cc_final: 0.5799 (ptm) REVERT: A 83 ASP cc_start: 0.8009 (m-30) cc_final: 0.7720 (m-30) REVERT: A 105 TYR cc_start: 0.8168 (m-80) cc_final: 0.7909 (m-80) REVERT: A 128 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7539 (ttm170) REVERT: A 193 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 250 GLN cc_start: 0.6555 (pt0) cc_final: 0.6019 (pm20) REVERT: A 290 HIS cc_start: 0.0849 (OUTLIER) cc_final: 0.0137 (t-90) REVERT: B 82 LEU cc_start: 0.8314 (mt) cc_final: 0.7976 (mp) REVERT: C 28 TYR cc_start: 0.8524 (t80) cc_final: 0.7949 (t80) REVERT: D 52 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7432 (tm130) REVERT: E 67 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8056 (mtmt) REVERT: F 37 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7334 (tttp) REVERT: F 43 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7017 (mp0) outliers start: 33 outliers final: 24 residues processed: 189 average time/residue: 0.2624 time to fit residues: 66.5168 Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 73 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.239405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.183017 restraints weight = 12850.105| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.76 r_work: 0.3888 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10901 Z= 0.170 Angle : 0.653 9.298 15453 Z= 0.326 Chirality : 0.036 0.190 1836 Planarity : 0.004 0.036 1396 Dihedral : 22.924 175.430 3381 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.08 % Favored : 92.58 % Rotamer: Outliers : 3.90 % Allowed : 24.19 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 876 helix: 0.47 (0.20), residues: 662 sheet: -1.90 (0.91), residues: 24 loop : -2.36 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.013 0.001 HIS A 121 PHE 0.026 0.002 PHE A 260 TYR 0.024 0.002 TYR A 58 ARG 0.008 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 596) hydrogen bonds : angle 4.61190 ( 1608) covalent geometry : bond 0.00395 (10901) covalent geometry : angle 0.65256 (15453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7235 (mmt) cc_final: 0.5764 (ptm) REVERT: A 40 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 83 ASP cc_start: 0.8004 (m-30) cc_final: 0.7714 (m-30) REVERT: A 193 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 250 GLN cc_start: 0.6532 (pt0) cc_final: 0.6035 (pm20) REVERT: A 290 HIS cc_start: 0.0853 (OUTLIER) cc_final: 0.0115 (t-90) REVERT: B 11 TYR cc_start: 0.6883 (t80) cc_final: 0.6641 (t80) REVERT: D 18 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7050 (tt0) REVERT: D 52 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7617 (tm130) REVERT: E 67 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8056 (mtmt) REVERT: F 37 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7310 (tttp) REVERT: F 43 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7058 (mp0) outliers start: 29 outliers final: 23 residues processed: 180 average time/residue: 0.2596 time to fit residues: 63.3726 Evaluate side-chains 181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 96 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.238114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181690 restraints weight = 12802.847| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.78 r_work: 0.3854 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10901 Z= 0.198 Angle : 0.680 10.258 15453 Z= 0.341 Chirality : 0.037 0.186 1836 Planarity : 0.005 0.036 1396 Dihedral : 22.868 175.186 3381 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.08 % Favored : 92.58 % Rotamer: Outliers : 3.90 % Allowed : 24.46 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 876 helix: 0.41 (0.20), residues: 662 sheet: -1.83 (0.93), residues: 24 loop : -2.37 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.013 0.001 HIS A 121 PHE 0.028 0.002 PHE B 80 TYR 0.025 0.003 TYR A 58 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 596) hydrogen bonds : angle 4.66653 ( 1608) covalent geometry : bond 0.00466 (10901) covalent geometry : angle 0.67974 (15453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7206 (mmt) cc_final: 0.5772 (ptm) REVERT: A 75 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5612 (tm) REVERT: A 128 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: A 193 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7494 (t80) REVERT: A 250 GLN cc_start: 0.6518 (pt0) cc_final: 0.6132 (pm20) REVERT: A 290 HIS cc_start: 0.0817 (OUTLIER) cc_final: -0.0106 (t-90) REVERT: D 52 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7683 (tm130) REVERT: E 67 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8016 (mtmt) REVERT: F 43 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7030 (mp0) outliers start: 29 outliers final: 21 residues processed: 181 average time/residue: 0.2566 time to fit residues: 63.4758 Evaluate side-chains 182 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.241435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.185986 restraints weight = 12520.481| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.65 r_work: 0.3922 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10901 Z= 0.192 Angle : 0.688 10.231 15453 Z= 0.342 Chirality : 0.037 0.183 1836 Planarity : 0.005 0.036 1396 Dihedral : 22.832 175.083 3381 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.08 % Favored : 92.58 % Rotamer: Outliers : 3.76 % Allowed : 24.46 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.28), residues: 876 helix: 0.38 (0.19), residues: 661 sheet: -1.58 (0.97), residues: 24 loop : -2.29 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.014 0.001 HIS A 121 PHE 0.025 0.002 PHE B 80 TYR 0.024 0.002 TYR A 58 ARG 0.013 0.001 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 596) hydrogen bonds : angle 4.71343 ( 1608) covalent geometry : bond 0.00451 (10901) covalent geometry : angle 0.68833 (15453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5904.51 seconds wall clock time: 104 minutes 19.12 seconds (6259.12 seconds total)