Starting phenix.real_space_refine on Thu May 1 03:40:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub9_42079/05_2025/8ub9_42079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub9_42079/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub9_42079/05_2025/8ub9_42079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub9_42079/05_2025/8ub9_42079.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub9_42079/05_2025/8ub9_42079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub9_42079/05_2025/8ub9_42079.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.07, per 1000 atoms: 0.68 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: 2.63 Conformation dependent library (CDL) restraints added in 925.2 milliseconds 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: 4.76 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: 3.40 Time building geometry restraints manager: 3.12 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.920 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (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 TRP 0.069 0.010 TRP C 116 HIS 0.016 0.004 HIS A 160 PHE 0.050 0.009 PHE D 84 TYR 0.066 0.010 TYR C 28 ARG 0.040 0.003 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.19233 ( 608) hydrogen bonds : angle 8.47926 ( 1634) covalent geometry : bond 0.01149 (10902) covalent geometry : angle 1.28852 (15451) *********************** 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 : 0.903 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: 0.4559 (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: 0.7319 (tp30) REVERT: A 82 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7703 (ptpp) 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: 0.8022 (tp30) REVERT: B 64 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6248 (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: 0.7985 (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: 0.3155 time to fit residues: 131.6229 Evaluate side-chains 228 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.168785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123805 restraints weight = 13875.471| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.95 r_work: 0.3398 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10902 Z= 0.182 Angle : 0.687 7.813 15451 Z= 0.352 Chirality : 0.040 0.290 1834 Planarity : 0.006 0.123 1402 Dihedral : 23.750 179.723 3435 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.04 % Favored : 92.51 % Rotamer: Outliers : 6.83 % Allowed : 19.54 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.27), residues: 881 helix: -0.24 (0.19), residues: 676 sheet: -3.65 (0.91), residues: 24 loop : -3.52 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 318 HIS 0.008 0.001 HIS A 133 PHE 0.029 0.002 PHE A 231 TYR 0.019 0.002 TYR C 69 ARG 0.005 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 608) hydrogen bonds : angle 4.71154 ( 1634) covalent geometry : bond 0.00399 (10902) covalent geometry : angle 0.68669 (15451) *********************** 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: 51 poor density : 206 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6590 (mmm) cc_final: 0.5661 (mtt) REVERT: A 33 TRP cc_start: 0.8186 (t-100) cc_final: 0.7805 (t60) REVERT: A 37 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 47 LEU cc_start: 0.8567 (mt) cc_final: 0.8287 (mt) REVERT: A 65 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: A 80 GLU cc_start: 0.7792 (mp0) cc_final: 0.7554 (mp0) REVERT: A 140 SER cc_start: 0.8183 (p) cc_final: 0.7716 (p) REVERT: A 141 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7353 (mmtm) REVERT: A 226 GLU cc_start: 0.8379 (tp30) cc_final: 0.8163 (tp30) REVERT: A 232 TYR cc_start: 0.8589 (m-10) cc_final: 0.8287 (m-80) REVERT: A 258 ILE cc_start: 0.8518 (mt) cc_final: 0.8273 (mt) REVERT: A 290 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.6042 (m-70) REVERT: B 9 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7853 (mtmm) REVERT: B 13 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 22 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7742 (mtp-110) REVERT: B 77 MET cc_start: 0.8357 (tpt) cc_final: 0.8101 (tpt) REVERT: C 19 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8116 (tpp-160) REVERT: C 20 TYR cc_start: 0.8203 (t80) cc_final: 0.7917 (t80) REVERT: D 103 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7674 (mm-40) REVERT: F 14 MET cc_start: 0.5865 (mmp) cc_final: 0.5622 (tmm) REVERT: F 20 TYR cc_start: 0.8217 (t80) cc_final: 0.7936 (t80) REVERT: F 21 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6901 (mt-10) REVERT: F 25 SER cc_start: 0.9085 (t) cc_final: 0.8753 (m) REVERT: F 30 ILE cc_start: 0.8239 (pt) cc_final: 0.7945 (pt) REVERT: F 68 LEU cc_start: 0.8381 (mt) cc_final: 0.8129 (mt) outliers start: 51 outliers final: 19 residues processed: 241 average time/residue: 0.2921 time to fit residues: 92.2619 Evaluate side-chains 196 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 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 7 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122454 restraints weight = 14152.250| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.97 r_work: 0.3374 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10902 Z= 0.182 Angle : 0.650 11.288 15451 Z= 0.328 Chirality : 0.038 0.186 1834 Planarity : 0.006 0.146 1402 Dihedral : 23.055 176.811 3366 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.13 % Favored : 93.30 % Rotamer: Outliers : 4.55 % Allowed : 19.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 881 helix: 0.28 (0.19), residues: 664 sheet: -1.26 (1.52), residues: 14 loop : -2.97 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 210 HIS 0.007 0.001 HIS B 38 PHE 0.024 0.002 PHE A 231 TYR 0.016 0.002 TYR D 26 ARG 0.004 0.001 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 608) hydrogen bonds : angle 4.46820 ( 1634) covalent geometry : bond 0.00412 (10902) covalent geometry : angle 0.65009 (15451) *********************** 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 224 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6896 (mmm) cc_final: 0.6235 (mpp) REVERT: A 33 TRP cc_start: 0.8244 (t-100) cc_final: 0.7878 (t60) REVERT: A 37 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 47 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 65 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: A 75 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4301 (tm) REVERT: A 80 GLU cc_start: 0.7967 (mp0) cc_final: 0.7397 (mp0) REVERT: A 83 ASP cc_start: 0.8949 (m-30) cc_final: 0.8388 (m-30) REVERT: A 140 SER cc_start: 0.7961 (p) cc_final: 0.7429 (p) REVERT: A 141 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7478 (mmtm) REVERT: A 232 TYR cc_start: 0.8654 (m-10) cc_final: 0.8340 (m-80) REVERT: A 254 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 258 ILE cc_start: 0.8659 (mt) cc_final: 0.8402 (mt) REVERT: B 9 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7922 (mtmm) REVERT: B 14 MET cc_start: 0.8394 (mtt) cc_final: 0.8092 (mtt) REVERT: B 22 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7664 (mtp-110) REVERT: B 64 GLN cc_start: 0.7583 (tt0) cc_final: 0.7078 (tt0) REVERT: B 66 SER cc_start: 0.8999 (t) cc_final: 0.8538 (p) REVERT: B 77 MET cc_start: 0.8346 (tpt) cc_final: 0.8054 (tpt) REVERT: C 19 ARG cc_start: 0.8312 (tpp80) cc_final: 0.8039 (tpp-160) REVERT: D 19 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7887 (tpp80) REVERT: D 22 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7511 (mtm110) REVERT: E 44 MET cc_start: 0.8589 (mtp) cc_final: 0.8274 (mtp) REVERT: E 92 HIS cc_start: 0.7757 (m90) cc_final: 0.7521 (m90) REVERT: F 20 TYR cc_start: 0.8298 (t80) cc_final: 0.7920 (t80) REVERT: F 25 SER cc_start: 0.8960 (t) cc_final: 0.8712 (m) outliers start: 34 outliers final: 15 residues processed: 216 average time/residue: 0.2791 time to fit residues: 79.6905 Evaluate side-chains 189 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 E residue 43 GLU 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 11 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.168194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122676 restraints weight = 14053.891| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.96 r_work: 0.3377 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10902 Z= 0.175 Angle : 0.635 13.773 15451 Z= 0.319 Chirality : 0.037 0.181 1834 Planarity : 0.006 0.154 1402 Dihedral : 22.877 175.969 3359 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.47 % Favored : 93.08 % Rotamer: Outliers : 3.75 % Allowed : 21.55 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 881 helix: 0.41 (0.19), residues: 664 sheet: -0.01 (1.56), residues: 14 loop : -2.79 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 116 HIS 0.007 0.001 HIS B 38 PHE 0.022 0.002 PHE A 231 TYR 0.016 0.002 TYR D 26 ARG 0.005 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05113 ( 608) hydrogen bonds : angle 4.34026 ( 1634) covalent geometry : bond 0.00394 (10902) covalent geometry : angle 0.63528 (15451) *********************** 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 201 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.961 Fit side-chains REVERT: A 1 MET cc_start: 0.6924 (mmm) cc_final: 0.6355 (mpp) REVERT: A 33 TRP cc_start: 0.8166 (t-100) cc_final: 0.7591 (t60) REVERT: A 37 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7808 (pp20) REVERT: A 47 LEU cc_start: 0.8501 (mt) cc_final: 0.8239 (mt) REVERT: A 75 LEU cc_start: 0.5160 (OUTLIER) cc_final: 0.4586 (pp) REVERT: A 83 ASP cc_start: 0.8958 (m-30) cc_final: 0.8633 (m-30) REVERT: A 232 TYR cc_start: 0.8624 (m-10) cc_final: 0.8256 (m-80) REVERT: A 254 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7790 (p) REVERT: A 258 ILE cc_start: 0.8577 (mt) cc_final: 0.8334 (mt) REVERT: A 261 LEU cc_start: 0.8961 (mt) cc_final: 0.8740 (tp) REVERT: A 319 MET cc_start: 0.7942 (mtp) cc_final: 0.7346 (tmm) REVERT: B 9 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8053 (mtmm) REVERT: B 22 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7750 (mtp-110) REVERT: B 61 LYS cc_start: 0.8999 (mmtp) cc_final: 0.8658 (mmmt) REVERT: B 64 GLN cc_start: 0.7633 (tt0) cc_final: 0.7168 (tt0) REVERT: B 66 SER cc_start: 0.8982 (t) cc_final: 0.8526 (p) REVERT: B 77 MET cc_start: 0.8361 (tpt) cc_final: 0.8122 (tpt) REVERT: C 19 ARG cc_start: 0.8265 (tpp80) cc_final: 0.8056 (tpp-160) REVERT: D 22 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7442 (mtm110) REVERT: D 69 TYR cc_start: 0.7601 (m-80) cc_final: 0.7395 (m-80) REVERT: E 44 MET cc_start: 0.8700 (mtp) cc_final: 0.8425 (mtp) REVERT: F 20 TYR cc_start: 0.8272 (t80) cc_final: 0.7874 (t80) REVERT: F 25 SER cc_start: 0.9008 (t) cc_final: 0.8699 (m) outliers start: 28 outliers final: 14 residues processed: 197 average time/residue: 0.2689 time to fit residues: 70.7866 Evaluate side-chains 179 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 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 D residue 40 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 11 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** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.168093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123195 restraints weight = 14110.974| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.94 r_work: 0.3384 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4893 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= 0.174 Angle : 0.633 8.244 15451 Z= 0.318 Chirality : 0.036 0.181 1834 Planarity : 0.006 0.132 1402 Dihedral : 22.758 175.427 3354 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.79 % Favored : 93.76 % Rotamer: Outliers : 4.15 % Allowed : 21.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 881 helix: 0.51 (0.19), residues: 664 sheet: 0.44 (1.55), residues: 14 loop : -2.45 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 116 HIS 0.004 0.001 HIS B 38 PHE 0.022 0.002 PHE A 231 TYR 0.016 0.002 TYR D 26 ARG 0.006 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 608) hydrogen bonds : angle 4.30510 ( 1634) covalent geometry : bond 0.00394 (10902) covalent geometry : angle 0.63326 (15451) *********************** 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 203 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6969 (mmm) cc_final: 0.6660 (mpp) REVERT: A 33 TRP cc_start: 0.8173 (t-100) cc_final: 0.7692 (t60) REVERT: A 37 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: A 47 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8270 (mt) REVERT: A 75 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4685 (pp) REVERT: A 83 ASP cc_start: 0.8957 (m-30) cc_final: 0.8598 (m-30) REVERT: A 232 TYR cc_start: 0.8599 (m-10) cc_final: 0.8234 (m-80) REVERT: A 254 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 258 ILE cc_start: 0.8587 (mt) cc_final: 0.8317 (mt) REVERT: A 319 MET cc_start: 0.7939 (mtp) cc_final: 0.7335 (tmm) REVERT: B 9 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8121 (mtmm) REVERT: B 61 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8705 (mmmt) REVERT: B 64 GLN cc_start: 0.7648 (tt0) cc_final: 0.7156 (tt0) REVERT: B 66 SER cc_start: 0.8986 (t) cc_final: 0.8519 (p) REVERT: B 77 MET cc_start: 0.8345 (tpt) cc_final: 0.8101 (tpt) REVERT: C 19 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8042 (tpp-160) REVERT: D 22 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7447 (mtm110) REVERT: D 69 TYR cc_start: 0.7584 (m-80) cc_final: 0.7335 (m-80) REVERT: E 44 MET cc_start: 0.8750 (mtp) cc_final: 0.8520 (mtp) REVERT: F 20 TYR cc_start: 0.8339 (t80) cc_final: 0.7894 (t80) REVERT: F 25 SER cc_start: 0.8988 (t) cc_final: 0.8666 (m) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.2870 time to fit residues: 73.7215 Evaluate side-chains 183 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 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 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 46 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125552 restraints weight = 14191.308| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.99 r_work: 0.3417 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10902 Z= 0.148 Angle : 0.615 7.637 15451 Z= 0.310 Chirality : 0.036 0.220 1834 Planarity : 0.006 0.123 1402 Dihedral : 22.645 175.833 3354 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.02 % Favored : 93.53 % Rotamer: Outliers : 3.75 % Allowed : 22.49 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 881 helix: 0.68 (0.20), residues: 664 sheet: 0.46 (1.51), residues: 14 loop : -2.36 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.005 0.001 HIS B 38 PHE 0.020 0.002 PHE A 231 TYR 0.014 0.002 TYR C 20 ARG 0.006 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 608) hydrogen bonds : angle 4.25836 ( 1634) covalent geometry : bond 0.00330 (10902) covalent geometry : angle 0.61533 (15451) *********************** 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 199 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6981 (mmm) cc_final: 0.6560 (mpp) REVERT: A 33 TRP cc_start: 0.8104 (t-100) cc_final: 0.7693 (t60) REVERT: A 47 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 75 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.5213 (pp) REVERT: A 83 ASP cc_start: 0.8927 (m-30) cc_final: 0.8556 (m-30) REVERT: A 232 TYR cc_start: 0.8565 (m-10) cc_final: 0.8166 (m-80) REVERT: A 258 ILE cc_start: 0.8570 (mt) cc_final: 0.8303 (mt) REVERT: A 319 MET cc_start: 0.7868 (mtp) cc_final: 0.7295 (tmm) REVERT: B 9 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8044 (mtmm) REVERT: B 64 GLN cc_start: 0.7650 (tt0) cc_final: 0.7134 (tt0) REVERT: B 66 SER cc_start: 0.8963 (t) cc_final: 0.8473 (p) REVERT: B 77 MET cc_start: 0.8293 (tpt) cc_final: 0.8089 (tpt) REVERT: C 19 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7992 (tpp-160) REVERT: D 22 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7422 (mtm110) REVERT: D 69 TYR cc_start: 0.7569 (m-80) cc_final: 0.7303 (m-80) REVERT: E 44 MET cc_start: 0.8729 (mtp) cc_final: 0.8517 (mtp) REVERT: F 20 TYR cc_start: 0.8278 (t80) cc_final: 0.7835 (t80) REVERT: F 25 SER cc_start: 0.8935 (t) cc_final: 0.8631 (m) REVERT: F 26 TYR cc_start: 0.8343 (t80) cc_final: 0.8071 (t80) outliers start: 28 outliers final: 18 residues processed: 195 average time/residue: 0.2692 time to fit residues: 70.6505 Evaluate side-chains 178 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 43 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR 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 66 SER Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 79 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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** E 92 HIS ** F 38 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.171749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127722 restraints weight = 14346.950| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.96 r_work: 0.3445 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10902 Z= 0.138 Angle : 0.619 16.531 15451 Z= 0.306 Chirality : 0.036 0.195 1834 Planarity : 0.006 0.164 1402 Dihedral : 22.514 176.032 3349 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.22 % Favored : 94.32 % Rotamer: Outliers : 3.35 % Allowed : 23.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 881 helix: 0.83 (0.20), residues: 664 sheet: 0.69 (1.55), residues: 14 loop : -2.40 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.006 0.001 HIS B 38 PHE 0.020 0.002 PHE A 231 TYR 0.015 0.002 TYR C 28 ARG 0.008 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 608) hydrogen bonds : angle 4.21763 ( 1634) covalent geometry : bond 0.00302 (10902) covalent geometry : angle 0.61863 (15451) *********************** 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: 25 poor density : 168 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6945 (mmm) cc_final: 0.6117 (mpp) REVERT: A 33 TRP cc_start: 0.8008 (t-100) cc_final: 0.7643 (t60) REVERT: A 37 GLU cc_start: 0.8163 (pt0) cc_final: 0.7329 (mt-10) REVERT: A 47 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8264 (mt) REVERT: A 75 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.5207 (pp) REVERT: A 83 ASP cc_start: 0.8926 (m-30) cc_final: 0.8566 (m-30) REVERT: A 232 TYR cc_start: 0.8548 (m-10) cc_final: 0.8185 (m-80) REVERT: A 258 ILE cc_start: 0.8506 (mt) cc_final: 0.8262 (mt) REVERT: A 319 MET cc_start: 0.7912 (mtp) cc_final: 0.7296 (tmm) REVERT: B 9 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7974 (mtmm) REVERT: B 69 TYR cc_start: 0.8457 (m-80) cc_final: 0.7907 (m-10) REVERT: B 77 MET cc_start: 0.8238 (tpt) cc_final: 0.8030 (tpt) REVERT: B 83 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: C 19 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7997 (tpp-160) REVERT: D 22 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7432 (mtm110) REVERT: D 69 TYR cc_start: 0.7464 (m-80) cc_final: 0.7192 (m-80) REVERT: E 44 MET cc_start: 0.8728 (mtp) cc_final: 0.8492 (mtp) REVERT: F 20 TYR cc_start: 0.8253 (t80) cc_final: 0.7831 (t80) REVERT: F 25 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8533 (m) outliers start: 25 outliers final: 13 residues processed: 187 average time/residue: 0.2618 time to fit residues: 65.9914 Evaluate side-chains 170 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 C residue 90 LYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** A 306 HIS 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 = 0.4175 r_free = 0.4175 target = 0.172831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128198 restraints weight = 14107.017| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.97 r_work: 0.3454 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10902 Z= 0.142 Angle : 0.626 14.375 15451 Z= 0.309 Chirality : 0.036 0.172 1834 Planarity : 0.006 0.145 1402 Dihedral : 22.437 175.775 3348 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.56 % Favored : 93.98 % Rotamer: Outliers : 2.68 % Allowed : 24.10 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 881 helix: 0.86 (0.20), residues: 665 sheet: 0.77 (1.54), residues: 14 loop : -2.45 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 PHE 0.020 0.002 PHE A 231 TYR 0.017 0.002 TYR C 20 ARG 0.007 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 608) hydrogen bonds : angle 4.14240 ( 1634) covalent geometry : bond 0.00316 (10902) covalent geometry : angle 0.62630 (15451) *********************** 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 184 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6963 (mmm) cc_final: 0.6160 (mpp) REVERT: A 33 TRP cc_start: 0.7907 (t-100) cc_final: 0.7548 (t60) REVERT: A 37 GLU cc_start: 0.8109 (pt0) cc_final: 0.7240 (mt-10) REVERT: A 47 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 83 ASP cc_start: 0.8915 (m-30) cc_final: 0.8564 (m-30) REVERT: A 232 TYR cc_start: 0.8538 (m-10) cc_final: 0.8181 (m-80) REVERT: A 258 ILE cc_start: 0.8491 (mt) cc_final: 0.8247 (mt) REVERT: A 273 ARG cc_start: 0.6293 (ttm-80) cc_final: 0.6079 (mtt-85) REVERT: A 319 MET cc_start: 0.7919 (mtp) cc_final: 0.7300 (tmm) REVERT: B 9 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7994 (mtmm) REVERT: B 69 TYR cc_start: 0.8504 (m-80) cc_final: 0.7927 (m-10) REVERT: B 77 MET cc_start: 0.8280 (tpt) cc_final: 0.8005 (tpt) REVERT: B 83 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8029 (mtm-85) REVERT: C 13 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6491 (tm130) REVERT: C 19 ARG cc_start: 0.8221 (tpp80) cc_final: 0.8017 (tpp-160) REVERT: C 44 MET cc_start: 0.8440 (mtp) cc_final: 0.8118 (mtp) REVERT: D 22 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7431 (mtm110) REVERT: D 69 TYR cc_start: 0.7435 (m-80) cc_final: 0.7164 (m-80) REVERT: E 44 MET cc_start: 0.8740 (mtp) cc_final: 0.8539 (mtp) REVERT: F 20 TYR cc_start: 0.8269 (t80) cc_final: 0.7904 (t80) outliers start: 20 outliers final: 14 residues processed: 179 average time/residue: 0.2647 time to fit residues: 63.5595 Evaluate side-chains 176 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 13 GLN Chi-restraints excluded: chain C residue 30 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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** ** 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 = 0.4170 r_free = 0.4170 target = 0.171723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127059 restraints weight = 14253.311| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.98 r_work: 0.3449 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10902 Z= 0.155 Angle : 0.664 14.051 15451 Z= 0.327 Chirality : 0.036 0.208 1834 Planarity : 0.005 0.058 1402 Dihedral : 22.411 175.501 3344 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.13 % Favored : 93.53 % Rotamer: Outliers : 2.54 % Allowed : 24.63 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 881 helix: 0.85 (0.20), residues: 665 sheet: 0.84 (1.55), residues: 14 loop : -2.51 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.011 0.001 HIS F 92 PHE 0.020 0.002 PHE A 231 TYR 0.015 0.002 TYR A 105 ARG 0.011 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 608) hydrogen bonds : angle 4.17454 ( 1634) covalent geometry : bond 0.00350 (10902) covalent geometry : angle 0.66430 (15451) *********************** 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 183 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7098 (mmm) cc_final: 0.6776 (mpp) REVERT: A 33 TRP cc_start: 0.7984 (t-100) cc_final: 0.7623 (t60) REVERT: A 37 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: A 47 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 83 ASP cc_start: 0.8906 (m-30) cc_final: 0.8565 (m-30) REVERT: A 232 TYR cc_start: 0.8537 (m-10) cc_final: 0.8170 (m-80) REVERT: A 254 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7442 (p) REVERT: A 258 ILE cc_start: 0.8537 (mt) cc_final: 0.8292 (mt) REVERT: A 273 ARG cc_start: 0.6476 (ttm-80) cc_final: 0.6250 (mtt-85) REVERT: A 319 MET cc_start: 0.7790 (mtp) cc_final: 0.7265 (tmm) REVERT: B 9 LYS cc_start: 0.8283 (mtmm) cc_final: 0.8033 (mtmm) REVERT: B 66 SER cc_start: 0.8929 (t) cc_final: 0.8617 (p) REVERT: B 77 MET cc_start: 0.8299 (tpt) cc_final: 0.8037 (tpt) REVERT: C 18 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 19 ARG cc_start: 0.8288 (tpp80) cc_final: 0.8014 (tpp-160) REVERT: D 22 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7451 (mtm110) REVERT: D 69 TYR cc_start: 0.7432 (m-80) cc_final: 0.7153 (m-80) REVERT: F 20 TYR cc_start: 0.8336 (t80) cc_final: 0.7995 (t80) outliers start: 19 outliers final: 13 residues processed: 179 average time/residue: 0.2521 time to fit residues: 61.7966 Evaluate side-chains 171 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 92 HIS Chi-restraints excluded: chain C residue 94 MET 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 F residue 15 LEU 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 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.0010 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 64 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.173082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.128902 restraints weight = 14161.181| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.95 r_work: 0.3466 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5853 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= 0.147 Angle : 0.659 14.031 15451 Z= 0.325 Chirality : 0.036 0.226 1834 Planarity : 0.005 0.058 1402 Dihedral : 22.394 175.683 3344 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.13 % Favored : 93.53 % Rotamer: Outliers : 2.41 % Allowed : 24.50 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 881 helix: 0.87 (0.20), residues: 666 sheet: 1.02 (1.57), residues: 14 loop : -2.52 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.014 0.001 HIS F 92 PHE 0.019 0.002 PHE A 231 TYR 0.014 0.002 TYR C 69 ARG 0.010 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 608) hydrogen bonds : angle 4.20908 ( 1634) covalent geometry : bond 0.00326 (10902) covalent geometry : angle 0.65856 (15451) ********************** 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 176 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7079 (mmm) cc_final: 0.6810 (mpp) REVERT: A 33 TRP cc_start: 0.7914 (t-100) cc_final: 0.7578 (t60) REVERT: A 37 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 47 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 83 ASP cc_start: 0.8875 (m-30) cc_final: 0.8517 (m-30) REVERT: A 232 TYR cc_start: 0.8531 (m-10) cc_final: 0.8123 (m-80) REVERT: A 254 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7472 (p) REVERT: A 258 ILE cc_start: 0.8534 (mt) cc_final: 0.8290 (mt) REVERT: A 273 ARG cc_start: 0.6484 (ttm-80) cc_final: 0.6271 (mtt-85) REVERT: A 319 MET cc_start: 0.7775 (mtp) cc_final: 0.7248 (tmm) REVERT: B 66 SER cc_start: 0.8913 (t) cc_final: 0.8651 (p) REVERT: B 69 TYR cc_start: 0.8492 (m-80) cc_final: 0.7998 (m-10) REVERT: B 77 MET cc_start: 0.8286 (tpt) cc_final: 0.8029 (tpt) REVERT: B 83 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: C 13 GLN cc_start: 0.7469 (tm130) cc_final: 0.6861 (tp40) REVERT: C 18 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 19 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7972 (tpp-160) REVERT: C 44 MET cc_start: 0.8442 (mtp) cc_final: 0.8192 (mtp) REVERT: D 22 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7445 (mtm110) REVERT: D 69 TYR cc_start: 0.7490 (m-80) cc_final: 0.7211 (m-80) REVERT: E 44 MET cc_start: 0.8616 (mtp) cc_final: 0.8343 (mtp) REVERT: E 67 LYS cc_start: 0.8470 (mttm) cc_final: 0.7892 (mttt) REVERT: F 19 ARG cc_start: 0.8279 (tpp80) cc_final: 0.8036 (tpp-160) REVERT: F 20 TYR cc_start: 0.8277 (t80) cc_final: 0.7959 (t80) outliers start: 18 outliers final: 14 residues processed: 171 average time/residue: 0.3032 time to fit residues: 71.8619 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 : 0.810 ------------------------------------------------------------------------------- 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 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 C residue 94 MET 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 F residue 15 LEU 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 80 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 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 64 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126590 restraints weight = 14111.979| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.96 r_work: 0.3439 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10902 Z= 0.175 Angle : 0.672 13.065 15451 Z= 0.333 Chirality : 0.037 0.232 1834 Planarity : 0.005 0.060 1402 Dihedral : 22.398 175.165 3344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.90 % Favored : 93.76 % Rotamer: Outliers : 2.41 % Allowed : 24.90 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 881 helix: 0.77 (0.20), residues: 666 sheet: 0.86 (1.58), residues: 14 loop : -2.55 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 210 HIS 0.012 0.001 HIS F 92 PHE 0.020 0.002 PHE A 231 TYR 0.027 0.002 TYR A 105 ARG 0.009 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 608) hydrogen bonds : angle 4.28872 ( 1634) covalent geometry : bond 0.00398 (10902) covalent geometry : angle 0.67164 (15451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.28 seconds wall clock time: 91 minutes 28.15 seconds (5488.15 seconds total)