Starting phenix.real_space_refine on Sat Aug 23 06:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2025/8ub9_42079.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 148 5.49 5 S 36 5.16 5 C 6064 2.51 5 N 1868 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10370 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} 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: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10370 At special positions: 0 Unit cell: (81, 105, 133, 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 148 15.00 O 2254 8.00 N 1868 7.00 C 6064 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: 1.13 Conformation dependent library (CDL) restraints added in 314.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 76.8% alpha, 2.8% beta 47 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.528A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.897A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.556A 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 202 removed outlier: 4.137A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.602A pdb=" N LYS A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.626A 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 307 removed outlier: 3.902A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.678A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.524A 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 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.525A 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: 3.722A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.671A 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' 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 88 removed outlier: 3.502A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.771A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.514A 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 34 removed outlier: 3.686A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.631A 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 62 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.595A 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 34 removed outlier: 3.519A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.617A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) 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: 3.526A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.740A pdb=" N HIS F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 93 " --> pdb=" O LYS F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.252A 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: 4.047A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265 488 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1572 1.32 - 1.45: 3780 1.45 - 1.57: 5193 1.57 - 1.70: 296 1.70 - 1.82: 61 Bond restraints: 10902 Sorted by residual: bond pdb=" O3' U G 378 " pdb=" P G G 379 " ideal model delta sigma weight residual 1.607 1.454 0.153 1.50e-02 4.44e+03 1.04e+02 bond pdb=" CA ASN F 63 " pdb=" CB ASN F 63 " ideal model delta sigma weight residual 1.531 1.642 -0.111 1.51e-02 4.39e+03 5.43e+01 bond pdb=" CA ARG B 111 " pdb=" CB ARG B 111 " ideal model delta sigma weight residual 1.529 1.432 0.097 1.55e-02 4.16e+03 3.93e+01 bond pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.50e-02 4.44e+03 2.58e+01 bond pdb=" CA LEU F 15 " pdb=" CB LEU F 15 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.74e-02 3.30e+03 2.09e+01 ... (remaining 10897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14570 2.53 - 5.07: 799 5.07 - 7.60: 71 7.60 - 10.13: 9 10.13 - 12.67: 2 Bond angle restraints: 15451 Sorted by residual: angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 94.01 9.24 1.05e+00 9.07e-01 7.74e+01 angle pdb=" C3' U I 67 " pdb=" O3' U I 67 " pdb=" P C I 68 " ideal model delta sigma weight residual 120.20 107.53 12.67 1.50e+00 4.44e-01 7.13e+01 angle pdb=" C3' U I 24 " pdb=" O3' U I 24 " pdb=" P U I 25 " ideal model delta sigma weight residual 120.20 107.68 12.52 1.50e+00 4.44e-01 6.97e+01 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 111.71 104.08 7.63 1.34e+00 5.57e-01 3.24e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 111.71 105.58 6.13 1.15e+00 7.56e-01 2.84e+01 ... (remaining 15446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 5956 35.34 - 70.68: 736 70.68 - 106.02: 68 106.02 - 141.35: 3 141.35 - 176.69: 3 Dihedral angle restraints: 6766 sinusoidal: 4167 harmonic: 2599 Sorted by residual: 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 55.31 176.69 1 1.70e+01 3.46e-03 6.64e+01 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 56.20 175.80 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C5' A I 56 " pdb=" C4' A I 56 " pdb=" C3' A I 56 " pdb=" O3' A I 56 " ideal model delta sinusoidal sigma weight residual 147.00 106.03 40.97 1 8.00e+00 1.56e-02 3.67e+01 ... (remaining 6763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1466 0.117 - 0.234: 335 0.234 - 0.351: 22 0.351 - 0.468: 6 0.468 - 0.585: 5 Chirality restraints: 1834 Sorted by residual: 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 -3.00 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.75e+00 ... (remaining 1831 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.066 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR C 28 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 156 " -0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C ASP A 156 " 0.082 2.00e-02 2.50e+03 pdb=" O ASP A 156 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 157 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " 0.048 2.00e-02 2.50e+03 2.88e-02 1.86e+01 pdb=" N1 U I 7 " -0.063 2.00e-02 2.50e+03 pdb=" C2 U I 7 " -0.011 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U I 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U I 7 " 0.024 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U I 7 " -0.004 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1148 2.73 - 3.27: 10655 3.27 - 3.82: 22194 3.82 - 4.36: 27636 4.36 - 4.90: 38981 Nonbonded interactions: 100614 Sorted by model distance: nonbonded pdb=" O2' A I 100 " pdb=" OP2 A I 101 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.222 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.238 3.040 nonbonded pdb=" O GLN F 32 " pdb=" N2 G I 4 " model vdw 2.243 3.120 nonbonded pdb=" O ILE A 159 " pdb=" N CYS A 161 " model vdw 2.246 3.120 ... (remaining 100609 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.153 10902 Z= 0.668 Angle : 1.289 12.666 15451 Z= 0.794 Chirality : 0.099 0.585 1834 Planarity : 0.010 0.098 1402 Dihedral : 24.954 176.692 5090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 2.95 % Allowed : 9.31 % Favored : 87.74 % Rotamer: Outliers : 18.47 % Allowed : 14.32 % Favored : 67.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.23), residues: 881 helix: -1.69 (0.17), residues: 666 sheet: -4.58 (0.90), residues: 22 loop : -4.15 (0.34), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.003 ARG C 42 TYR 0.066 0.010 TYR C 28 PHE 0.050 0.009 PHE D 84 TRP 0.069 0.010 TRP C 116 HIS 0.016 0.004 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.01149 (10902) covalent geometry : angle 1.28852 (15451) hydrogen bonds : bond 0.19233 ( 608) hydrogen bonds : angle 8.47926 ( 1634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 245 time to evaluate : 0.310 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: 0.5424 (mmm) cc_final: 0.4558 (mtt) REVERT: A 4 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7166 (ttp-110) REVERT: A 7 ASN cc_start: 0.8536 (m-40) cc_final: 0.8101 (m110) REVERT: A 65 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: A 82 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7706 (pttm) REVERT: A 92 ASN cc_start: 0.9021 (m-40) cc_final: 0.8807 (m110) REVERT: A 140 SER cc_start: 0.8184 (p) cc_final: 0.7972 (t) REVERT: A 141 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7486 (mmtm) REVERT: A 158 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7778 (tppt) REVERT: A 175 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: A 222 ASP cc_start: 0.8162 (p0) cc_final: 0.7502 (m-30) REVERT: A 223 ASP cc_start: 0.8810 (t70) cc_final: 0.8602 (t0) REVERT: A 232 TYR cc_start: 0.8437 (m-10) cc_final: 0.8088 (m-80) REVERT: A 258 ILE cc_start: 0.8846 (mt) cc_final: 0.8607 (mt) REVERT: B 21 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8532 (tt0) REVERT: B 22 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7444 (mtm110) REVERT: B 54 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: B 64 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: B 77 MET cc_start: 0.8348 (tpt) cc_final: 0.8086 (tpt) REVERT: C 18 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8219 (pt0) REVERT: C 21 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7986 (mt-10) REVERT: D 55 LEU cc_start: 0.8321 (mt) cc_final: 0.8086 (mp) REVERT: D 103 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: D 116 TRP cc_start: 0.8083 (t60) cc_final: 0.7811 (t60) REVERT: E 14 MET cc_start: 0.7833 (mmt) cc_final: 0.7445 (mtt) REVERT: E 54 GLU cc_start: 0.7477 (tt0) cc_final: 0.7174 (tp30) REVERT: E 89 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6534 (mt0) REVERT: F 14 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5539 (tmm) REVERT: F 20 TYR cc_start: 0.8397 (t80) cc_final: 0.7728 (t80) REVERT: F 21 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7932 (mt-10) REVERT: F 27 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 55 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7921 (mp) REVERT: F 65 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7423 (p) REVERT: F 113 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8279 (tp) outliers start: 138 outliers final: 29 residues processed: 327 average time/residue: 0.1575 time to fit residues: 65.3426 Evaluate side-chains 229 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 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 32 GLN B 64 GLN B 89 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN D 64 GLN ** F 92 HIS ** 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 = 0.4138 r_free = 0.4138 target = 0.169021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124334 restraints weight = 14016.827| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.93 r_work: 0.3391 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10902 Z= 0.188 Angle : 0.692 7.819 15451 Z= 0.355 Chirality : 0.040 0.289 1834 Planarity : 0.006 0.123 1402 Dihedral : 23.750 179.545 3435 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.04 % Favored : 92.51 % Rotamer: Outliers : 6.96 % Allowed : 18.88 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.27), residues: 881 helix: -0.26 (0.19), residues: 676 sheet: -3.64 (0.92), residues: 24 loop : -3.52 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.019 0.002 TYR C 69 PHE 0.030 0.002 PHE A 231 TRP 0.012 0.002 TRP A 318 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00420 (10902) covalent geometry : angle 0.69242 (15451) hydrogen bonds : bond 0.05501 ( 608) hydrogen bonds : angle 4.71335 ( 1634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6594 (mmm) cc_final: 0.5667 (mtt) REVERT: A 33 TRP cc_start: 0.8197 (t-100) cc_final: 0.7864 (t60) REVERT: A 37 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: A 47 LEU cc_start: 0.8548 (mt) cc_final: 0.8266 (mt) REVERT: A 65 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: A 80 GLU cc_start: 0.7784 (mp0) cc_final: 0.7522 (mp0) REVERT: A 92 ASN cc_start: 0.8921 (m-40) cc_final: 0.8642 (m-40) REVERT: A 140 SER cc_start: 0.8181 (p) cc_final: 0.7715 (p) REVERT: A 141 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7341 (mmtm) REVERT: A 226 GLU cc_start: 0.8396 (tp30) cc_final: 0.8172 (tp30) REVERT: A 232 TYR cc_start: 0.8622 (m-10) cc_final: 0.8314 (m-80) REVERT: A 258 ILE cc_start: 0.8510 (mt) cc_final: 0.8261 (mt) REVERT: A 290 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.6043 (m-70) REVERT: B 9 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7846 (mtmm) REVERT: B 14 MET cc_start: 0.8278 (mtt) cc_final: 0.7969 (mtt) REVERT: B 22 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7739 (mtp-110) REVERT: B 77 MET cc_start: 0.8363 (tpt) cc_final: 0.8133 (tpt) REVERT: C 19 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8125 (tpp-160) REVERT: C 20 TYR cc_start: 0.8213 (t80) cc_final: 0.7924 (t80) REVERT: D 103 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7666 (mm-40) REVERT: F 14 MET cc_start: 0.5845 (mmp) cc_final: 0.5607 (tmm) REVERT: F 20 TYR cc_start: 0.8225 (t80) cc_final: 0.7844 (t80) REVERT: F 21 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6891 (mt-10) REVERT: F 25 SER cc_start: 0.9079 (t) cc_final: 0.8746 (m) REVERT: F 30 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7982 (pt) REVERT: F 44 MET cc_start: 0.8991 (mtp) cc_final: 0.8725 (mtp) REVERT: F 68 LEU cc_start: 0.8376 (mt) cc_final: 0.8137 (mt) outliers start: 52 outliers final: 19 residues processed: 240 average time/residue: 0.1132 time to fit residues: 35.7867 Evaluate side-chains 193 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.167464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122426 restraints weight = 14197.051| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.96 r_work: 0.3375 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10902 Z= 0.183 Angle : 0.650 9.899 15451 Z= 0.329 Chirality : 0.038 0.187 1834 Planarity : 0.006 0.143 1402 Dihedral : 23.071 176.705 3366 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.47 % Favored : 92.96 % Rotamer: Outliers : 4.82 % Allowed : 18.88 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.27), residues: 881 helix: 0.27 (0.19), residues: 665 sheet: -1.17 (1.52), residues: 14 loop : -2.95 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.017 0.002 TYR D 26 PHE 0.024 0.002 PHE A 231 TRP 0.009 0.002 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00415 (10902) covalent geometry : angle 0.65008 (15451) hydrogen bonds : bond 0.05193 ( 608) hydrogen bonds : angle 4.45476 ( 1634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6890 (mmm) cc_final: 0.6249 (mpp) REVERT: A 33 TRP cc_start: 0.8259 (t-100) cc_final: 0.7881 (t60) REVERT: A 37 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: A 47 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 65 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: A 75 LEU cc_start: 0.5133 (OUTLIER) cc_final: 0.4279 (tm) REVERT: A 83 ASP cc_start: 0.8940 (m-30) cc_final: 0.8625 (m-30) REVERT: A 92 ASN cc_start: 0.8940 (m-40) cc_final: 0.8632 (m-40) REVERT: A 140 SER cc_start: 0.7978 (p) cc_final: 0.7438 (p) REVERT: A 141 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7555 (mmtm) REVERT: A 232 TYR cc_start: 0.8657 (m-10) cc_final: 0.8348 (m-80) REVERT: A 254 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 258 ILE cc_start: 0.8663 (mt) cc_final: 0.8412 (mt) REVERT: A 283 LYS cc_start: 0.8327 (mttm) cc_final: 0.8119 (mtpp) REVERT: B 9 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7937 (mtmm) REVERT: B 14 MET cc_start: 0.8244 (mtt) cc_final: 0.7977 (mtt) REVERT: B 22 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7645 (mtp-110) REVERT: B 64 GLN cc_start: 0.7613 (tt0) cc_final: 0.7094 (tt0) REVERT: B 66 SER cc_start: 0.8957 (t) cc_final: 0.8487 (p) REVERT: B 67 LYS cc_start: 0.8340 (mttm) cc_final: 0.7803 (mtmm) REVERT: B 77 MET cc_start: 0.8350 (tpt) cc_final: 0.8060 (tpt) REVERT: B 83 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: C 19 ARG cc_start: 0.8309 (tpp80) cc_final: 0.8032 (tpp-160) REVERT: D 19 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7899 (tpp80) REVERT: D 22 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7513 (mtm110) REVERT: D 103 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7440 (mm-40) REVERT: E 19 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8346 (ttm110) REVERT: E 44 MET cc_start: 0.8618 (mtp) cc_final: 0.8288 (mtp) REVERT: E 92 HIS cc_start: 0.7768 (m90) cc_final: 0.7531 (m90) REVERT: F 14 MET cc_start: 0.5242 (mmp) cc_final: 0.5040 (tmm) REVERT: F 20 TYR cc_start: 0.8294 (t80) cc_final: 0.7922 (t80) REVERT: F 25 SER cc_start: 0.8965 (t) cc_final: 0.8713 (m) REVERT: F 44 MET cc_start: 0.9071 (mtp) cc_final: 0.8791 (mtp) outliers start: 36 outliers final: 16 residues processed: 218 average time/residue: 0.1117 time to fit residues: 32.3184 Evaluate side-chains 194 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121021 restraints weight = 14167.573| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.99 r_work: 0.3352 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10902 Z= 0.203 Angle : 0.656 13.230 15451 Z= 0.329 Chirality : 0.038 0.187 1834 Planarity : 0.006 0.153 1402 Dihedral : 22.941 175.464 3362 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.47 % Favored : 93.08 % Rotamer: Outliers : 4.42 % Allowed : 20.48 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.28), residues: 881 helix: 0.30 (0.19), residues: 667 sheet: -0.04 (1.56), residues: 14 loop : -2.77 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 111 TYR 0.018 0.002 TYR D 26 PHE 0.023 0.002 PHE A 231 TRP 0.017 0.002 TRP E 116 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00461 (10902) covalent geometry : angle 0.65583 (15451) hydrogen bonds : bond 0.05222 ( 608) hydrogen bonds : angle 4.40619 ( 1634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.252 Fit side-chains REVERT: A 1 MET cc_start: 0.6891 (mmm) cc_final: 0.6369 (mpp) REVERT: A 33 TRP cc_start: 0.8249 (t-100) cc_final: 0.7650 (t60) REVERT: A 37 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7827 (pp20) REVERT: A 47 LEU cc_start: 0.8538 (mt) cc_final: 0.8253 (mt) REVERT: A 65 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 75 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4617 (pp) REVERT: A 83 ASP cc_start: 0.8967 (m-30) cc_final: 0.8603 (m-30) REVERT: A 92 ASN cc_start: 0.8939 (m-40) cc_final: 0.8667 (m-40) REVERT: A 232 TYR cc_start: 0.8644 (m-10) cc_final: 0.8311 (m-80) REVERT: A 254 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 258 ILE cc_start: 0.8602 (mt) cc_final: 0.8362 (mt) REVERT: A 261 LEU cc_start: 0.8986 (mt) cc_final: 0.8742 (tt) REVERT: A 274 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7943 (ttmm) REVERT: A 319 MET cc_start: 0.7979 (mtp) cc_final: 0.7377 (tmm) REVERT: B 9 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8109 (mtmm) REVERT: B 22 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7750 (mtp-110) REVERT: B 61 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8679 (mmmt) REVERT: B 64 GLN cc_start: 0.7650 (tt0) cc_final: 0.7193 (tt0) REVERT: B 66 SER cc_start: 0.9020 (t) cc_final: 0.8547 (p) REVERT: B 67 LYS cc_start: 0.8329 (mttm) cc_final: 0.7806 (mttp) REVERT: B 77 MET cc_start: 0.8412 (tpt) cc_final: 0.8163 (tpt) REVERT: C 19 ARG cc_start: 0.8329 (tpp80) cc_final: 0.8113 (tpp-160) REVERT: D 19 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7891 (tpp80) REVERT: D 22 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7456 (mtm110) REVERT: D 69 TYR cc_start: 0.7648 (m-80) cc_final: 0.7424 (m-80) REVERT: D 103 GLN cc_start: 0.7893 (mt0) cc_final: 0.7522 (mm-40) REVERT: D 111 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7946 (mtm-85) REVERT: E 19 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8327 (ttm110) REVERT: E 44 MET cc_start: 0.8733 (mtp) cc_final: 0.8530 (mtp) REVERT: E 67 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7643 (mttt) REVERT: E 92 HIS cc_start: 0.7878 (m90) cc_final: 0.7668 (m90) REVERT: F 14 MET cc_start: 0.5462 (mmp) cc_final: 0.5151 (tmm) REVERT: F 20 TYR cc_start: 0.8343 (t80) cc_final: 0.7967 (t80) REVERT: F 25 SER cc_start: 0.9027 (t) cc_final: 0.8696 (m) outliers start: 33 outliers final: 21 residues processed: 198 average time/residue: 0.1071 time to fit residues: 28.0405 Evaluate side-chains 191 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 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 197 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.167449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121594 restraints weight = 14135.199| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.97 r_work: 0.3365 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10902 Z= 0.187 Angle : 0.638 8.615 15451 Z= 0.321 Chirality : 0.037 0.184 1834 Planarity : 0.006 0.131 1402 Dihedral : 22.817 175.056 3357 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.13 % Favored : 93.42 % Rotamer: Outliers : 4.69 % Allowed : 20.48 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.28), residues: 881 helix: 0.43 (0.19), residues: 667 sheet: 0.15 (1.49), residues: 14 loop : -2.60 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.018 0.002 TYR C 69 PHE 0.023 0.002 PHE A 231 TRP 0.011 0.001 TRP E 116 HIS 0.011 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00428 (10902) covalent geometry : angle 0.63794 (15451) hydrogen bonds : bond 0.05151 ( 608) hydrogen bonds : angle 4.34613 ( 1634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6976 (mmm) cc_final: 0.6506 (mpp) REVERT: A 33 TRP cc_start: 0.8201 (t-100) cc_final: 0.7730 (t60) REVERT: A 37 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: A 47 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8265 (mt) REVERT: A 75 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4685 (pp) REVERT: A 83 ASP cc_start: 0.8970 (m-30) cc_final: 0.8665 (m-30) REVERT: A 92 ASN cc_start: 0.8906 (m-40) cc_final: 0.8678 (m-40) REVERT: A 232 TYR cc_start: 0.8625 (m-10) cc_final: 0.8249 (m-80) REVERT: A 254 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7823 (p) REVERT: A 258 ILE cc_start: 0.8586 (mt) cc_final: 0.8315 (mt) REVERT: A 274 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7936 (ttmm) REVERT: A 319 MET cc_start: 0.7923 (mtp) cc_final: 0.7293 (tmm) REVERT: B 9 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8111 (mtmm) REVERT: B 22 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7750 (mtp-110) REVERT: B 61 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8632 (mmmt) REVERT: B 64 GLN cc_start: 0.7657 (tt0) cc_final: 0.7181 (tt0) REVERT: B 66 SER cc_start: 0.9013 (t) cc_final: 0.8523 (p) REVERT: B 77 MET cc_start: 0.8370 (tpt) cc_final: 0.8124 (tpt) REVERT: C 19 ARG cc_start: 0.8305 (tpp80) cc_final: 0.8072 (tpp-160) REVERT: D 69 TYR cc_start: 0.7609 (m-80) cc_final: 0.7358 (m-80) REVERT: D 103 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: E 19 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8250 (ttm110) REVERT: F 14 MET cc_start: 0.5666 (mmp) cc_final: 0.5196 (tmm) REVERT: F 20 TYR cc_start: 0.8317 (t80) cc_final: 0.7845 (t80) REVERT: F 25 SER cc_start: 0.9006 (t) cc_final: 0.8645 (m) outliers start: 35 outliers final: 22 residues processed: 199 average time/residue: 0.1072 time to fit residues: 28.2787 Evaluate side-chains 189 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 62 optimal weight: 0.0050 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127789 restraints weight = 14281.629| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.94 r_work: 0.3444 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10902 Z= 0.138 Angle : 0.598 7.604 15451 Z= 0.302 Chirality : 0.036 0.208 1834 Planarity : 0.006 0.121 1402 Dihedral : 22.564 176.224 3354 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.21 % Rotamer: Outliers : 4.15 % Allowed : 22.22 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.28), residues: 881 helix: 0.69 (0.20), residues: 666 sheet: 0.77 (1.51), residues: 14 loop : -2.39 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.016 0.001 TYR C 69 PHE 0.021 0.002 PHE A 231 TRP 0.018 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00306 (10902) covalent geometry : angle 0.59811 (15451) hydrogen bonds : bond 0.05067 ( 608) hydrogen bonds : angle 4.23097 ( 1634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6801 (mmm) cc_final: 0.6105 (mpp) REVERT: A 33 TRP cc_start: 0.8043 (t-100) cc_final: 0.7652 (t60) REVERT: A 37 GLU cc_start: 0.8163 (pt0) cc_final: 0.7329 (mt-10) REVERT: A 47 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 75 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5163 (pp) REVERT: A 83 ASP cc_start: 0.8914 (m-30) cc_final: 0.8541 (m-30) REVERT: A 92 ASN cc_start: 0.8848 (m-40) cc_final: 0.8572 (m-40) REVERT: A 232 TYR cc_start: 0.8564 (m-10) cc_final: 0.8208 (m-80) REVERT: A 258 ILE cc_start: 0.8525 (mt) cc_final: 0.8283 (mt) REVERT: A 274 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7772 (ttmm) REVERT: A 319 MET cc_start: 0.7904 (mtp) cc_final: 0.7307 (tmm) REVERT: B 9 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8036 (mtmm) REVERT: B 61 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8598 (mmmt) REVERT: B 64 GLN cc_start: 0.7696 (tt0) cc_final: 0.7177 (tt0) REVERT: B 66 SER cc_start: 0.8882 (t) cc_final: 0.8390 (p) REVERT: B 77 MET cc_start: 0.8272 (tpt) cc_final: 0.8034 (tpt) REVERT: C 19 ARG cc_start: 0.8229 (tpp80) cc_final: 0.8008 (tpp-160) REVERT: D 69 TYR cc_start: 0.7571 (m-80) cc_final: 0.7326 (m-80) REVERT: D 103 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7592 (mm-40) REVERT: E 44 MET cc_start: 0.8531 (mtp) cc_final: 0.8283 (mtp) REVERT: E 67 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7822 (mttt) REVERT: F 14 MET cc_start: 0.5399 (mmp) cc_final: 0.5143 (tmm) REVERT: F 20 TYR cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: F 25 SER cc_start: 0.8895 (t) cc_final: 0.8529 (m) outliers start: 31 outliers final: 16 residues processed: 204 average time/residue: 0.1032 time to fit residues: 28.1725 Evaluate side-chains 176 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 121 ASN C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.172215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128071 restraints weight = 14189.765| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.94 r_work: 0.3446 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10902 Z= 0.142 Angle : 0.620 15.920 15451 Z= 0.307 Chirality : 0.036 0.226 1834 Planarity : 0.006 0.163 1402 Dihedral : 22.499 175.679 3348 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.79 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 21.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.28), residues: 881 helix: 0.75 (0.20), residues: 666 sheet: 0.96 (1.58), residues: 14 loop : -2.43 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.021 0.002 TYR A 105 PHE 0.020 0.002 PHE A 231 TRP 0.014 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00315 (10902) covalent geometry : angle 0.62007 (15451) hydrogen bonds : bond 0.05038 ( 608) hydrogen bonds : angle 4.20921 ( 1634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6896 (mmm) cc_final: 0.6103 (mpp) REVERT: A 33 TRP cc_start: 0.7946 (t-100) cc_final: 0.7577 (t60) REVERT: A 37 GLU cc_start: 0.8112 (pt0) cc_final: 0.7272 (mt-10) REVERT: A 47 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 75 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.5095 (pp) REVERT: A 83 ASP cc_start: 0.8932 (m-30) cc_final: 0.8575 (m-30) REVERT: A 92 ASN cc_start: 0.8873 (m-40) cc_final: 0.8608 (m-40) REVERT: A 232 TYR cc_start: 0.8559 (m-10) cc_final: 0.8192 (m-80) REVERT: A 258 ILE cc_start: 0.8587 (mt) cc_final: 0.8333 (mt) REVERT: A 274 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7768 (ttmm) REVERT: A 319 MET cc_start: 0.7906 (mtp) cc_final: 0.7293 (tmm) REVERT: B 9 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7934 (mtmm) REVERT: B 64 GLN cc_start: 0.7621 (tt0) cc_final: 0.7083 (tt0) REVERT: B 66 SER cc_start: 0.8912 (t) cc_final: 0.8464 (p) REVERT: B 77 MET cc_start: 0.8266 (tpt) cc_final: 0.8034 (tpt) REVERT: D 22 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7437 (mtm110) REVERT: D 69 TYR cc_start: 0.7505 (m-80) cc_final: 0.7246 (m-80) REVERT: E 44 MET cc_start: 0.8620 (mtp) cc_final: 0.8301 (mtp) REVERT: E 67 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7825 (mttt) REVERT: F 14 MET cc_start: 0.5403 (mmp) cc_final: 0.5127 (tmm) REVERT: F 20 TYR cc_start: 0.8332 (t80) cc_final: 0.8001 (t80) REVERT: F 25 SER cc_start: 0.8967 (t) cc_final: 0.8516 (m) outliers start: 30 outliers final: 16 residues processed: 185 average time/residue: 0.1082 time to fit residues: 26.7203 Evaluate side-chains 177 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125344 restraints weight = 14190.727| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.93 r_work: 0.3417 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10902 Z= 0.171 Angle : 0.652 12.783 15451 Z= 0.323 Chirality : 0.036 0.225 1834 Planarity : 0.006 0.144 1402 Dihedral : 22.491 174.675 3346 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.90 % Favored : 93.64 % Rotamer: Outliers : 2.95 % Allowed : 22.49 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.28), residues: 881 helix: 0.73 (0.20), residues: 666 sheet: 0.68 (1.55), residues: 14 loop : -2.49 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.017 0.002 TYR A 105 PHE 0.021 0.002 PHE A 231 TRP 0.013 0.001 TRP A 210 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00392 (10902) covalent geometry : angle 0.65218 (15451) hydrogen bonds : bond 0.05176 ( 608) hydrogen bonds : angle 4.24603 ( 1634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7133 (mmm) cc_final: 0.6364 (mpp) REVERT: A 33 TRP cc_start: 0.7963 (t-100) cc_final: 0.7581 (t60) REVERT: A 37 GLU cc_start: 0.8153 (pt0) cc_final: 0.7291 (mt-10) REVERT: A 47 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8329 (mt) REVERT: A 83 ASP cc_start: 0.8925 (m-30) cc_final: 0.8640 (m-30) REVERT: A 232 TYR cc_start: 0.8542 (m-10) cc_final: 0.8148 (m-80) REVERT: A 254 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7681 (p) REVERT: A 258 ILE cc_start: 0.8578 (mt) cc_final: 0.8315 (mt) REVERT: A 274 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7798 (ttmm) REVERT: A 319 MET cc_start: 0.7812 (mtp) cc_final: 0.7235 (tmm) REVERT: B 9 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8014 (mtmm) REVERT: B 61 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8608 (mmmt) REVERT: B 64 GLN cc_start: 0.7665 (tt0) cc_final: 0.7297 (tt0) REVERT: B 66 SER cc_start: 0.8989 (t) cc_final: 0.8537 (p) REVERT: B 67 LYS cc_start: 0.8337 (mttm) cc_final: 0.7815 (mtmm) REVERT: B 77 MET cc_start: 0.8417 (tpt) cc_final: 0.8177 (tpt) REVERT: D 69 TYR cc_start: 0.7545 (m-80) cc_final: 0.7256 (m-80) REVERT: E 44 MET cc_start: 0.8709 (mtp) cc_final: 0.8409 (mtp) REVERT: E 67 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7852 (mttt) REVERT: F 14 MET cc_start: 0.5489 (mmp) cc_final: 0.5138 (tmm) REVERT: F 20 TYR cc_start: 0.8359 (t80) cc_final: 0.8007 (t80) REVERT: F 25 SER cc_start: 0.9008 (t) cc_final: 0.8442 (m) outliers start: 22 outliers final: 15 residues processed: 176 average time/residue: 0.1141 time to fit residues: 26.7002 Evaluate side-chains 168 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.171737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127618 restraints weight = 14186.589| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.94 r_work: 0.3448 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10902 Z= 0.147 Angle : 0.631 13.732 15451 Z= 0.313 Chirality : 0.036 0.220 1834 Planarity : 0.005 0.075 1402 Dihedral : 22.453 175.300 3344 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.02 % Favored : 93.64 % Rotamer: Outliers : 2.68 % Allowed : 23.83 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.29), residues: 881 helix: 0.78 (0.20), residues: 665 sheet: 0.76 (1.58), residues: 14 loop : -2.50 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.019 0.002 TYR C 69 PHE 0.020 0.002 PHE A 231 TRP 0.011 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00331 (10902) covalent geometry : angle 0.63069 (15451) hydrogen bonds : bond 0.05126 ( 608) hydrogen bonds : angle 4.19786 ( 1634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7030 (mmm) cc_final: 0.6748 (mpp) REVERT: A 33 TRP cc_start: 0.7901 (t-100) cc_final: 0.7541 (t60) REVERT: A 37 GLU cc_start: 0.8103 (pt0) cc_final: 0.7266 (mt-10) REVERT: A 47 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 83 ASP cc_start: 0.8904 (m-30) cc_final: 0.8561 (m-30) REVERT: A 92 ASN cc_start: 0.8888 (m-40) cc_final: 0.8622 (m-40) REVERT: A 232 TYR cc_start: 0.8535 (m-10) cc_final: 0.8166 (m-80) REVERT: A 254 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 258 ILE cc_start: 0.8586 (mt) cc_final: 0.8335 (mt) REVERT: A 273 ARG cc_start: 0.6604 (ttm-80) cc_final: 0.6161 (mtt-85) REVERT: A 274 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7807 (ttmm) REVERT: A 319 MET cc_start: 0.7784 (mtp) cc_final: 0.7219 (tmm) REVERT: B 61 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8598 (mmmt) REVERT: B 64 GLN cc_start: 0.7675 (tt0) cc_final: 0.7274 (tt0) REVERT: B 66 SER cc_start: 0.8953 (t) cc_final: 0.8496 (p) REVERT: B 67 LYS cc_start: 0.8315 (mttm) cc_final: 0.7795 (mtmm) REVERT: B 77 MET cc_start: 0.8349 (tpt) cc_final: 0.8116 (tpt) REVERT: C 18 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 44 MET cc_start: 0.8472 (mtp) cc_final: 0.8157 (mtp) REVERT: D 69 TYR cc_start: 0.7503 (m-80) cc_final: 0.7219 (m-80) REVERT: E 44 MET cc_start: 0.8719 (mtp) cc_final: 0.8412 (mtp) REVERT: E 67 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7926 (mttt) REVERT: F 14 MET cc_start: 0.5395 (mmp) cc_final: 0.5073 (tmm) REVERT: F 20 TYR cc_start: 0.8365 (t80) cc_final: 0.8041 (t80) outliers start: 20 outliers final: 14 residues processed: 176 average time/residue: 0.1208 time to fit residues: 28.0905 Evaluate side-chains 171 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 0.3980 chunk 10 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.173766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130275 restraints weight = 14141.010| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.93 r_work: 0.3493 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10902 Z= 0.132 Angle : 0.626 13.641 15451 Z= 0.311 Chirality : 0.035 0.223 1834 Planarity : 0.005 0.075 1402 Dihedral : 22.377 175.880 3344 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.02 % Favored : 93.64 % Rotamer: Outliers : 2.14 % Allowed : 23.83 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.29), residues: 881 helix: 0.85 (0.20), residues: 667 sheet: 1.07 (1.57), residues: 14 loop : -2.56 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.017 0.002 TYR A 105 PHE 0.019 0.002 PHE A 231 TRP 0.011 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00286 (10902) covalent geometry : angle 0.62579 (15451) hydrogen bonds : bond 0.05115 ( 608) hydrogen bonds : angle 4.18367 ( 1634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7829 (t-100) cc_final: 0.7488 (t60) REVERT: A 36 LEU cc_start: 0.7487 (mt) cc_final: 0.7256 (mm) REVERT: A 37 GLU cc_start: 0.8056 (pt0) cc_final: 0.7225 (mt-10) REVERT: A 47 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 83 ASP cc_start: 0.8864 (m-30) cc_final: 0.8497 (m-30) REVERT: A 92 ASN cc_start: 0.8859 (m-40) cc_final: 0.8552 (m-40) REVERT: A 232 TYR cc_start: 0.8508 (m-10) cc_final: 0.8118 (m-80) REVERT: A 258 ILE cc_start: 0.8603 (mt) cc_final: 0.8370 (mt) REVERT: A 273 ARG cc_start: 0.6561 (ttm-80) cc_final: 0.6222 (mtt-85) REVERT: A 274 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7773 (ttmm) REVERT: A 319 MET cc_start: 0.7768 (mtp) cc_final: 0.7240 (tmm) REVERT: B 64 GLN cc_start: 0.7773 (tt0) cc_final: 0.7335 (tt0) REVERT: B 66 SER cc_start: 0.8911 (t) cc_final: 0.8475 (p) REVERT: B 77 MET cc_start: 0.8338 (tpt) cc_final: 0.8127 (tpt) REVERT: C 18 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 44 MET cc_start: 0.8378 (mtp) cc_final: 0.8143 (mtp) REVERT: D 69 TYR cc_start: 0.7490 (m-80) cc_final: 0.7227 (m-80) REVERT: E 19 ARG cc_start: 0.8593 (ttm110) cc_final: 0.8196 (ttm110) REVERT: E 44 MET cc_start: 0.8692 (mtp) cc_final: 0.8371 (mtp) REVERT: E 67 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7942 (mttt) REVERT: F 14 MET cc_start: 0.5315 (mmp) cc_final: 0.5042 (tmm) REVERT: F 20 TYR cc_start: 0.8284 (t80) cc_final: 0.8004 (t80) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 0.1093 time to fit residues: 25.4920 Evaluate side-chains 171 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.170839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126373 restraints weight = 14095.064| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.93 r_work: 0.3427 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10902 Z= 0.180 Angle : 0.660 12.433 15451 Z= 0.330 Chirality : 0.036 0.209 1834 Planarity : 0.005 0.072 1402 Dihedral : 22.413 174.596 3344 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.02 % Favored : 93.53 % Rotamer: Outliers : 2.01 % Allowed : 24.10 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.29), residues: 881 helix: 0.74 (0.20), residues: 667 sheet: 0.86 (1.58), residues: 14 loop : -2.55 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 111 TYR 0.016 0.002 TYR C 69 PHE 0.020 0.002 PHE D 80 TRP 0.010 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00413 (10902) covalent geometry : angle 0.65961 (15451) hydrogen bonds : bond 0.05280 ( 608) hydrogen bonds : angle 4.27769 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.67 seconds wall clock time: 40 minutes 49.55 seconds (2449.55 seconds total)