Starting phenix.real_space_refine on Fri Feb 14 12:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub9_42079/02_2025/8ub9_42079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub9_42079/02_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_42079/02_2025/8ub9_42079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub9_42079/02_2025/8ub9_42079.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub9_42079/02_2025/8ub9_42079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub9_42079/02_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-5592/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: 6.58, per 1000 atoms: 0.63 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: 2.66 Conformation dependent library (CDL) restraints added in 852.2 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: 4.25 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: 3.53 Time building geometry restraints manager: 3.04 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- 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= 0.744 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 *********************** 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 : 0.839 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: 0.3341 time to fit residues: 139.6309 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 : 0.889 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123757 restraints weight = 13875.507| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.95 r_work: 0.3396 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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= 0.259 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 *********************** 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 : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6586 (mmm) cc_final: 0.5659 (mtt) REVERT: A 33 TRP cc_start: 0.8184 (t-100) cc_final: 0.7803 (t60) REVERT: A 37 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 47 LEU cc_start: 0.8565 (mt) cc_final: 0.8285 (mt) REVERT: A 65 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: A 80 GLU cc_start: 0.7791 (mp0) cc_final: 0.7553 (mp0) REVERT: A 140 SER cc_start: 0.8183 (p) cc_final: 0.7716 (p) REVERT: A 141 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7350 (mmtm) REVERT: A 226 GLU cc_start: 0.8381 (tp30) cc_final: 0.8165 (tp30) REVERT: A 232 TYR cc_start: 0.8589 (m-10) cc_final: 0.8287 (m-80) REVERT: A 258 ILE cc_start: 0.8517 (mt) cc_final: 0.8270 (mt) REVERT: A 290 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.6043 (m-70) REVERT: B 9 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7851 (mtmm) REVERT: B 13 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 22 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7739 (mtp-110) REVERT: B 77 MET cc_start: 0.8359 (tpt) cc_final: 0.8103 (tpt) REVERT: C 19 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8116 (tpp-160) REVERT: C 20 TYR cc_start: 0.8205 (t80) cc_final: 0.7918 (t80) REVERT: D 103 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (mm-40) REVERT: F 14 MET cc_start: 0.5862 (mmp) cc_final: 0.5622 (tmm) REVERT: F 20 TYR cc_start: 0.8215 (t80) cc_final: 0.7936 (t80) REVERT: F 21 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6902 (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: 0.8382 (mt) cc_final: 0.8130 (mt) outliers start: 51 outliers final: 19 residues processed: 241 average time/residue: 0.3045 time to fit residues: 95.9127 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 : 0.960 ------------------------------------------------------------------------------- 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: 0.1980 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4131 r_free = 0.4131 target = 0.168691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123433 restraints weight = 14153.670| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.97 r_work: 0.3389 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 0.060 10902 Z= 0.252 Angle : 0.641 11.455 15451 Z= 0.324 Chirality : 0.038 0.185 1834 Planarity : 0.006 0.148 1402 Dihedral : 23.061 177.209 3366 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.47 % Favored : 92.96 % Rotamer: Outliers : 4.69 % Allowed : 18.88 % Favored : 76.44 % 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: -0.73 (0.28), residues: 881 helix: 0.31 (0.19), residues: 664 sheet: -1.17 (1.54), residues: 14 loop : -2.95 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.008 0.001 HIS B 38 PHE 0.023 0.002 PHE A 231 TYR 0.016 0.002 TYR D 26 ARG 0.003 0.000 ARG E 36 *********************** 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 228 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6801 (mmm) cc_final: 0.6155 (mpp) REVERT: A 33 TRP cc_start: 0.8214 (t-100) cc_final: 0.7828 (t60) REVERT: A 37 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: A 47 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8253 (mt) REVERT: A 65 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: A 75 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4308 (tm) REVERT: A 80 GLU cc_start: 0.7945 (mp0) cc_final: 0.7419 (mp0) REVERT: A 83 ASP cc_start: 0.8911 (m-30) cc_final: 0.8311 (m-30) REVERT: A 140 SER cc_start: 0.7964 (p) cc_final: 0.7440 (p) REVERT: A 141 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7462 (mmtm) REVERT: A 232 TYR cc_start: 0.8643 (m-10) cc_final: 0.8345 (m-80) REVERT: A 258 ILE cc_start: 0.8663 (mt) cc_final: 0.8389 (mt) REVERT: B 9 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7919 (mtmm) REVERT: B 14 MET cc_start: 0.8381 (mtt) cc_final: 0.8073 (mtt) REVERT: B 22 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: B 64 GLN cc_start: 0.7595 (tt0) cc_final: 0.7121 (tt0) REVERT: B 66 SER cc_start: 0.8988 (t) cc_final: 0.8542 (p) REVERT: B 77 MET cc_start: 0.8345 (tpt) cc_final: 0.8056 (tpt) REVERT: B 83 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8112 (mtm-85) REVERT: C 19 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8027 (tpp-160) REVERT: D 22 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7492 (mtm110) REVERT: D 103 GLN cc_start: 0.7904 (mt0) cc_final: 0.7504 (mm-40) REVERT: E 44 MET cc_start: 0.8600 (mtp) cc_final: 0.8275 (mtp) REVERT: E 92 HIS cc_start: 0.7750 (m90) cc_final: 0.7520 (m90) REVERT: F 19 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8288 (tpp80) REVERT: F 20 TYR cc_start: 0.8289 (t80) cc_final: 0.7900 (t80) REVERT: F 25 SER cc_start: 0.9007 (t) cc_final: 0.8720 (m) outliers start: 35 outliers final: 15 residues processed: 221 average time/residue: 0.2858 time to fit residues: 83.6455 Evaluate side-chains 188 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 0.0470 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125707 restraints weight = 14111.857| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.98 r_work: 0.3426 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4825 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= 0.208 Angle : 0.619 11.593 15451 Z= 0.311 Chirality : 0.037 0.187 1834 Planarity : 0.006 0.147 1402 Dihedral : 22.794 176.738 3359 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.90 % Favored : 93.64 % Rotamer: Outliers : 4.42 % Allowed : 20.21 % Favored : 75.37 % 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: -0.31 (0.28), residues: 881 helix: 0.56 (0.19), residues: 664 sheet: 0.20 (1.57), residues: 14 loop : -2.72 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 116 HIS 0.005 0.001 HIS D 38 PHE 0.022 0.002 PHE A 231 TYR 0.015 0.002 TYR D 26 ARG 0.005 0.000 ARG F 111 *********************** 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 213 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6773 (mmm) cc_final: 0.6200 (mpp) REVERT: A 33 TRP cc_start: 0.8136 (t-100) cc_final: 0.7640 (t60) REVERT: A 37 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 47 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 75 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4639 (pp) REVERT: A 83 ASP cc_start: 0.8932 (m-30) cc_final: 0.8593 (m-30) REVERT: A 232 TYR cc_start: 0.8602 (m-10) cc_final: 0.8217 (m-80) REVERT: A 258 ILE cc_start: 0.8570 (mt) cc_final: 0.8290 (mt) REVERT: A 319 MET cc_start: 0.7909 (mtp) cc_final: 0.7318 (tmm) REVERT: B 9 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8067 (mtmm) REVERT: B 11 TYR cc_start: 0.8242 (t80) cc_final: 0.8036 (t80) REVERT: B 22 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7476 (mtm110) REVERT: B 61 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8619 (mmmt) REVERT: B 64 GLN cc_start: 0.7588 (tt0) cc_final: 0.7104 (tt0) REVERT: B 66 SER cc_start: 0.8932 (t) cc_final: 0.8457 (p) REVERT: B 77 MET cc_start: 0.8416 (tpt) cc_final: 0.8152 (tpt) REVERT: C 19 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7990 (tpp-160) REVERT: D 69 TYR cc_start: 0.7644 (m-80) cc_final: 0.7429 (m-80) REVERT: D 103 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7496 (mm-40) REVERT: E 44 MET cc_start: 0.8690 (mtp) cc_final: 0.8403 (mtp) REVERT: E 67 LYS cc_start: 0.8326 (mttm) cc_final: 0.7737 (mttt) REVERT: F 20 TYR cc_start: 0.8295 (t80) cc_final: 0.7887 (t80) REVERT: F 25 SER cc_start: 0.9033 (t) cc_final: 0.8704 (m) outliers start: 33 outliers final: 15 residues processed: 205 average time/residue: 0.2874 time to fit residues: 77.5249 Evaluate side-chains 182 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 66 SER 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 D 64 GLN E 92 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122704 restraints weight = 14117.439| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.97 r_work: 0.3370 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10902 Z= 0.284 Angle : 0.641 8.108 15451 Z= 0.320 Chirality : 0.037 0.180 1834 Planarity : 0.006 0.128 1402 Dihedral : 22.689 175.112 3354 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.47 % Favored : 93.08 % Rotamer: Outliers : 4.15 % Allowed : 21.29 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.28), residues: 881 helix: 0.56 (0.19), residues: 664 sheet: 0.42 (1.54), residues: 14 loop : -2.61 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 116 HIS 0.010 0.001 HIS B 38 PHE 0.022 0.002 PHE A 231 TYR 0.016 0.002 TYR D 26 ARG 0.007 0.000 ARG F 36 *********************** 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 207 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.999 Fit side-chains REVERT: A 1 MET cc_start: 0.7001 (mmm) cc_final: 0.6569 (mpp) REVERT: A 33 TRP cc_start: 0.8186 (t-100) cc_final: 0.7706 (t60) REVERT: A 37 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 47 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 75 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4861 (pp) REVERT: A 83 ASP cc_start: 0.8962 (m-30) cc_final: 0.8618 (m-30) REVERT: A 232 TYR cc_start: 0.8594 (m-10) cc_final: 0.8228 (m-80) REVERT: A 258 ILE cc_start: 0.8665 (mt) cc_final: 0.8436 (mt) REVERT: A 261 LEU cc_start: 0.8892 (tp) cc_final: 0.8608 (tp) REVERT: A 319 MET cc_start: 0.7939 (mtp) cc_final: 0.7330 (tmm) REVERT: B 9 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8110 (mtmm) REVERT: B 61 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8710 (mmmt) REVERT: B 64 GLN cc_start: 0.7650 (tt0) cc_final: 0.7141 (tt0) REVERT: B 66 SER cc_start: 0.8973 (t) cc_final: 0.8482 (p) REVERT: B 77 MET cc_start: 0.8418 (tpt) cc_final: 0.8168 (tpt) REVERT: C 19 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8066 (tpp-160) REVERT: D 22 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7460 (mtm110) REVERT: D 69 TYR cc_start: 0.7579 (m-80) cc_final: 0.7315 (m-80) REVERT: D 103 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7556 (mm-40) REVERT: E 44 MET cc_start: 0.8769 (mtp) cc_final: 0.8543 (mtp) REVERT: F 20 TYR cc_start: 0.8361 (t80) cc_final: 0.7941 (t80) REVERT: F 25 SER cc_start: 0.9017 (t) cc_final: 0.8670 (m) outliers start: 31 outliers final: 22 residues processed: 199 average time/residue: 0.2810 time to fit residues: 73.7360 Evaluate side-chains 190 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 33 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 D residue 103 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** 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 = 0.170327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124887 restraints weight = 14171.905| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.98 r_work: 0.3408 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5218 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= 0.231 Angle : 0.627 14.274 15451 Z= 0.310 Chirality : 0.036 0.192 1834 Planarity : 0.006 0.157 1402 Dihedral : 22.595 175.716 3354 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.56 % Favored : 93.98 % Rotamer: Outliers : 4.02 % Allowed : 21.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.28), residues: 881 helix: 0.67 (0.20), residues: 665 sheet: 0.37 (1.53), residues: 14 loop : -2.41 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 116 HIS 0.008 0.001 HIS B 38 PHE 0.021 0.002 PHE A 231 TYR 0.015 0.002 TYR C 20 ARG 0.008 0.000 ARG F 36 *********************** 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 204 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6922 (mmm) cc_final: 0.6525 (mpp) REVERT: A 33 TRP cc_start: 0.8132 (t-100) cc_final: 0.7709 (t60) REVERT: A 47 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 75 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5215 (pp) REVERT: A 83 ASP cc_start: 0.8939 (m-30) cc_final: 0.8577 (m-30) REVERT: A 232 TYR cc_start: 0.8557 (m-10) cc_final: 0.8153 (m-80) REVERT: A 258 ILE cc_start: 0.8625 (mt) cc_final: 0.8381 (mt) REVERT: A 261 LEU cc_start: 0.8803 (tp) cc_final: 0.8545 (tp) REVERT: A 319 MET cc_start: 0.7870 (mtp) cc_final: 0.7304 (tmm) REVERT: B 9 LYS cc_start: 0.8394 (mtmm) cc_final: 0.8056 (mtmm) REVERT: B 77 MET cc_start: 0.8369 (tpt) cc_final: 0.8123 (tpt) REVERT: C 19 ARG cc_start: 0.8259 (tpp80) cc_final: 0.8001 (tpp-160) REVERT: D 22 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7415 (mtm110) REVERT: D 69 TYR cc_start: 0.7473 (m-80) cc_final: 0.7181 (m-80) REVERT: D 103 GLN cc_start: 0.7866 (mt0) cc_final: 0.7617 (mm-40) REVERT: E 44 MET cc_start: 0.8715 (mtp) cc_final: 0.8474 (mtp) REVERT: F 20 TYR cc_start: 0.8282 (t80) cc_final: 0.7925 (t80) REVERT: F 25 SER cc_start: 0.9016 (t) cc_final: 0.8667 (m) outliers start: 30 outliers final: 20 residues processed: 199 average time/residue: 0.2865 time to fit residues: 75.2126 Evaluate side-chains 186 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 154 MET 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 C residue 90 LYS 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 65 VAL 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: 1.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125468 restraints weight = 14313.559| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.95 r_work: 0.3422 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10902 Z= 0.224 Angle : 0.626 9.826 15451 Z= 0.312 Chirality : 0.036 0.224 1834 Planarity : 0.006 0.137 1402 Dihedral : 22.522 175.593 3351 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.56 % Favored : 93.98 % Rotamer: Outliers : 3.61 % Allowed : 22.49 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.20), residues: 665 sheet: 0.75 (1.58), residues: 14 loop : -2.42 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.007 0.001 HIS B 38 PHE 0.020 0.002 PHE A 231 TYR 0.016 0.002 TYR C 28 ARG 0.009 0.000 ARG F 36 *********************** 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 196 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6988 (mmm) cc_final: 0.6158 (mpp) REVERT: A 33 TRP cc_start: 0.8133 (t-100) cc_final: 0.7717 (t60) REVERT: A 37 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 47 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 83 ASP cc_start: 0.8912 (m-30) cc_final: 0.8541 (m-30) REVERT: A 232 TYR cc_start: 0.8544 (m-10) cc_final: 0.8157 (m-80) REVERT: A 254 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7670 (p) REVERT: A 258 ILE cc_start: 0.8591 (mt) cc_final: 0.8340 (mt) REVERT: A 261 LEU cc_start: 0.8795 (tp) cc_final: 0.8535 (tp) REVERT: A 319 MET cc_start: 0.7902 (mtp) cc_final: 0.7326 (tmm) REVERT: B 9 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8078 (mtmm) REVERT: B 77 MET cc_start: 0.8360 (tpt) cc_final: 0.8112 (tpt) REVERT: C 19 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7977 (tpp-160) REVERT: D 22 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7414 (mtm110) REVERT: D 69 TYR cc_start: 0.7478 (m-80) cc_final: 0.7187 (m-80) REVERT: E 44 MET cc_start: 0.8728 (mtp) cc_final: 0.8512 (mtp) REVERT: F 20 TYR cc_start: 0.8281 (t80) cc_final: 0.7934 (t80) REVERT: F 25 SER cc_start: 0.9017 (t) cc_final: 0.8661 (m) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.2872 time to fit residues: 72.0143 Evaluate side-chains 179 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 154 MET 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 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 82 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.171463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126348 restraints weight = 14108.715| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.97 r_work: 0.3419 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10902 Z= 0.236 Angle : 0.651 10.715 15451 Z= 0.322 Chirality : 0.036 0.233 1834 Planarity : 0.006 0.128 1402 Dihedral : 22.475 175.451 3347 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.68 % Favored : 93.87 % Rotamer: Outliers : 2.81 % Allowed : 23.29 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.28), residues: 881 helix: 0.79 (0.20), residues: 666 sheet: 0.86 (1.61), residues: 14 loop : -2.45 (0.44), residues: 201 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 0.014 0.002 TYR C 28 ARG 0.005 0.000 ARG E 36 *********************** 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 185 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7008 (mmm) cc_final: 0.6184 (mpp) REVERT: A 33 TRP cc_start: 0.8095 (t-100) cc_final: 0.7710 (t60) REVERT: A 37 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 47 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 83 ASP cc_start: 0.8913 (m-30) cc_final: 0.8542 (m-30) REVERT: A 186 SER cc_start: 0.8482 (m) cc_final: 0.8151 (p) REVERT: A 232 TYR cc_start: 0.8542 (m-10) cc_final: 0.8151 (m-80) REVERT: A 254 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 258 ILE cc_start: 0.8562 (mt) cc_final: 0.8289 (mt) REVERT: A 261 LEU cc_start: 0.8765 (tp) cc_final: 0.8511 (tp) REVERT: A 319 MET cc_start: 0.7890 (mtp) cc_final: 0.7319 (tmm) REVERT: B 9 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7968 (mtmm) REVERT: B 66 SER cc_start: 0.8930 (t) cc_final: 0.8556 (p) REVERT: B 77 MET cc_start: 0.8308 (tpt) cc_final: 0.8020 (tpt) REVERT: B 83 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: C 13 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6564 (tm130) REVERT: C 19 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7989 (tpp-160) REVERT: D 22 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7392 (mtm110) REVERT: D 69 TYR cc_start: 0.7413 (m-80) cc_final: 0.7114 (m-80) REVERT: D 94 MET cc_start: 0.7902 (ttm) cc_final: 0.7597 (mtp) REVERT: E 44 MET cc_start: 0.8746 (mtp) cc_final: 0.8533 (mtp) REVERT: F 20 TYR cc_start: 0.8280 (t80) cc_final: 0.7910 (t80) REVERT: F 25 SER cc_start: 0.9026 (t) cc_final: 0.8650 (m) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.2808 time to fit residues: 66.4285 Evaluate side-chains 177 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 154 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 13 GLN 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 65 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 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 = 0.4161 r_free = 0.4161 target = 0.170845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126061 restraints weight = 14224.149| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.95 r_work: 0.3425 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10902 Z= 0.245 Angle : 0.652 9.629 15451 Z= 0.324 Chirality : 0.036 0.214 1834 Planarity : 0.006 0.125 1402 Dihedral : 22.462 175.321 3345 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.90 % Favored : 93.53 % Rotamer: Outliers : 2.81 % Allowed : 23.16 % 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: 0.08 (0.28), residues: 881 helix: 0.80 (0.20), residues: 666 sheet: 0.67 (1.61), residues: 14 loop : -2.43 (0.44), residues: 201 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 0.016 0.002 TYR A 105 ARG 0.007 0.000 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7132 (mmm) cc_final: 0.6321 (mpp) REVERT: A 33 TRP cc_start: 0.8118 (t-100) cc_final: 0.7756 (t60) REVERT: A 37 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 47 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 83 ASP cc_start: 0.8890 (m-30) cc_final: 0.8519 (m-30) REVERT: A 232 TYR cc_start: 0.8534 (m-10) cc_final: 0.8158 (m-80) REVERT: A 254 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 258 ILE cc_start: 0.8580 (mt) cc_final: 0.8333 (mt) REVERT: A 261 LEU cc_start: 0.8747 (tp) cc_final: 0.8503 (tp) REVERT: A 319 MET cc_start: 0.7875 (mtp) cc_final: 0.7327 (tmm) REVERT: B 9 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8000 (mtmm) REVERT: B 66 SER cc_start: 0.8897 (t) cc_final: 0.8622 (p) REVERT: B 77 MET cc_start: 0.8397 (tpt) cc_final: 0.8123 (tpt) REVERT: C 19 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7980 (tpp-160) REVERT: C 44 MET cc_start: 0.8538 (mtp) cc_final: 0.8195 (mtp) REVERT: D 22 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7421 (mtm110) REVERT: D 94 MET cc_start: 0.7888 (ttm) cc_final: 0.7604 (mtp) REVERT: E 44 MET cc_start: 0.8768 (mtp) cc_final: 0.8560 (mtp) REVERT: F 20 TYR cc_start: 0.8345 (t80) cc_final: 0.7938 (t80) REVERT: F 25 SER cc_start: 0.9053 (t) cc_final: 0.8681 (m) outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 0.2862 time to fit residues: 66.5653 Evaluate side-chains 174 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 94 MET 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 82 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: 0.9980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.171014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126291 restraints weight = 14158.279| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.96 r_work: 0.3428 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10902 Z= 0.242 Angle : 0.668 10.000 15451 Z= 0.330 Chirality : 0.036 0.227 1834 Planarity : 0.006 0.124 1402 Dihedral : 22.437 175.327 3345 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.90 % Favored : 93.53 % Rotamer: Outliers : 2.54 % Allowed : 23.56 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 881 helix: 0.82 (0.20), residues: 665 sheet: 0.67 (1.64), residues: 14 loop : -2.36 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.010 0.001 HIS F 92 PHE 0.020 0.002 PHE A 231 TYR 0.023 0.002 TYR C 69 ARG 0.007 0.000 ARG E 36 ********************** 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: 19 poor density : 157 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7110 (mmm) cc_final: 0.6784 (mpp) REVERT: A 33 TRP cc_start: 0.8102 (t-100) cc_final: 0.7731 (t60) REVERT: A 37 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: A 47 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 67 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4659 (pp) REVERT: A 83 ASP cc_start: 0.8889 (m-30) cc_final: 0.8524 (m-30) REVERT: A 232 TYR cc_start: 0.8534 (m-10) cc_final: 0.8154 (m-80) REVERT: A 254 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 258 ILE cc_start: 0.8587 (mt) cc_final: 0.8335 (mt) REVERT: A 261 LEU cc_start: 0.8733 (tp) cc_final: 0.8502 (tp) REVERT: A 319 MET cc_start: 0.7874 (mtp) cc_final: 0.7330 (tmm) REVERT: B 64 GLN cc_start: 0.7570 (tt0) cc_final: 0.7163 (tt0) REVERT: B 66 SER cc_start: 0.8959 (t) cc_final: 0.8576 (p) REVERT: B 77 MET cc_start: 0.8341 (tpt) cc_final: 0.8077 (tpt) REVERT: C 19 ARG cc_start: 0.8254 (tpp80) cc_final: 0.8046 (tpp-160) REVERT: C 44 MET cc_start: 0.8549 (mtp) cc_final: 0.8184 (mtp) REVERT: E 44 MET cc_start: 0.8761 (mtp) cc_final: 0.8560 (mtp) REVERT: F 20 TYR cc_start: 0.8343 (t80) cc_final: 0.7939 (t80) REVERT: F 25 SER cc_start: 0.9057 (t) cc_final: 0.8674 (m) outliers start: 19 outliers final: 13 residues processed: 172 average time/residue: 0.3097 time to fit residues: 71.1187 Evaluate side-chains 172 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 94 MET 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 82 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: 0.9990 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.170254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124993 restraints weight = 14100.216| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.96 r_work: 0.3411 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5723 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= 0.267 Angle : 0.668 9.281 15451 Z= 0.331 Chirality : 0.037 0.221 1834 Planarity : 0.006 0.123 1402 Dihedral : 22.452 174.958 3345 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.90 % Favored : 93.53 % Rotamer: Outliers : 2.68 % Allowed : 23.03 % Favored : 74.30 % 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: 0.02 (0.28), residues: 881 helix: 0.75 (0.20), residues: 666 sheet: 0.59 (1.64), residues: 14 loop : -2.45 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.011 0.001 HIS F 92 PHE 0.020 0.002 PHE A 231 TYR 0.020 0.002 TYR A 105 ARG 0.009 0.001 ARG F 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5022.85 seconds wall clock time: 90 minutes 43.38 seconds (5443.38 seconds total)