Starting phenix.real_space_refine on Sat Nov 16 03:14:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub7_42077/11_2024/8ub7_42077.cif" } resolution = 3.2 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 151 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1871 2.21 5 O 2267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10399 Number of models: 1 Model: "" Number of chains: 10 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 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.22, per 1000 atoms: 0.69 Number of scatterers: 10399 At special positions: 0 Unit cell: (81, 105, 134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 151 15.00 Mg 1 11.99 O 2267 8.00 N 1871 7.00 C 6073 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: 2.95 Conformation dependent library (CDL) restraints added in 935.2 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: 46 helices and 3 sheets defined 75.7% alpha, 2.6% beta 48 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.556A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.503A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) 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: 3.617A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 4.200A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) 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: 3.931A 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: 3.726A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.531A 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: 3.537A 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 32 removed outlier: 3.754A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.643A 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 removed outlier: 3.507A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.508A 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 32 removed outlier: 3.775A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.529A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.749A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.622A 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 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 66 through 86 removed outlier: 3.730A 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: 4.579A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.557A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' 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: 3.597A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.484A 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: 4.321A 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 265 474 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1406 1.32 - 1.45: 4069 1.45 - 1.58: 5098 1.58 - 1.71: 297 1.71 - 1.84: 61 Bond restraints: 10931 Sorted by residual: bond pdb=" C3' DCP A 401 " pdb=" C4' DCP A 401 " ideal model delta sigma weight residual 1.527 1.302 0.225 1.10e-02 8.26e+03 4.20e+02 bond pdb=" C1' DCP A 401 " pdb=" C2' DCP A 401 " ideal model delta sigma weight residual 1.521 1.356 0.165 1.20e-02 6.94e+03 1.90e+02 bond pdb=" O3A DCP A 401 " pdb=" PB DCP A 401 " ideal model delta sigma weight residual 1.592 1.698 -0.106 1.10e-02 8.26e+03 9.25e+01 bond pdb=" C4' DCP A 401 " pdb=" O4' DCP A 401 " ideal model delta sigma weight residual 1.444 1.540 -0.096 1.00e-02 1.00e+04 9.21e+01 bond pdb=" C2' DCP A 401 " pdb=" C3' DCP A 401 " ideal model delta sigma weight residual 1.523 1.626 -0.103 1.30e-02 5.92e+03 6.31e+01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13723 2.34 - 4.68: 1555 4.68 - 7.02: 186 7.02 - 9.35: 30 9.35 - 11.69: 2 Bond angle restraints: 15496 Sorted by residual: angle pdb=" PB DCP A 401 " pdb=" O3B DCP A 401 " pdb=" PG DCP A 401 " ideal model delta sigma weight residual 139.87 129.72 10.15 1.00e+00 1.00e+00 1.03e+02 angle pdb=" C ARG A 4 " pdb=" CA ARG A 4 " pdb=" CB ARG A 4 " ideal model delta sigma weight residual 116.54 107.41 9.13 1.15e+00 7.56e-01 6.30e+01 angle pdb=" C1' DCP A 401 " pdb=" O4' DCP A 401 " pdb=" C4' DCP A 401 " ideal model delta sigma weight residual 109.55 100.73 8.82 1.31e+00 5.82e-01 4.52e+01 angle pdb=" PA DCP A 401 " pdb=" O3A DCP A 401 " pdb=" PB DCP A 401 " ideal model delta sigma weight residual 136.83 130.27 6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" N ARG A 6 " pdb=" CA ARG A 6 " pdb=" C ARG A 6 " ideal model delta sigma weight residual 111.55 120.36 -8.81 1.37e+00 5.33e-01 4.13e+01 ... (remaining 15491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5936 35.16 - 70.32: 776 70.32 - 105.48: 76 105.48 - 140.64: 1 140.64 - 175.80: 4 Dihedral angle restraints: 6793 sinusoidal: 4194 harmonic: 2599 Sorted by residual: 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 87.25 59.75 1 8.00e+00 1.56e-02 7.44e+01 dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual -128.00 46.18 -174.18 1 1.70e+01 3.46e-03 6.63e+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 61.10 170.90 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 6790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1492 0.120 - 0.240: 303 0.240 - 0.360: 32 0.360 - 0.480: 6 0.480 - 0.600: 4 Chirality restraints: 1837 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 -3.01 -0.60 2.00e-01 2.50e+01 9.00e+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 -2.99 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 1834 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.081 2.00e-02 2.50e+03 4.09e-02 3.34e+01 pdb=" CG TYR C 28 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.066 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 U I 7 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.021 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U I 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.034 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO C 91 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.056 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1821 2.76 - 3.30: 10122 3.30 - 3.83: 21661 3.83 - 4.37: 26817 4.37 - 4.90: 37337 Nonbonded interactions: 97758 Sorted by model distance: nonbonded pdb=" OD2 ASP A 215 " pdb="MG MG A 402 " model vdw 2.230 2.170 nonbonded pdb=" O ILE A 159 " pdb=" N CYS A 161 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP A 138 " pdb="MG MG A 402 " model vdw 2.276 2.170 nonbonded pdb=" O ALA E 118 " pdb=" O ASN E 121 " model vdw 2.300 3.040 nonbonded pdb=" O PHE A 139 " pdb="MG MG A 402 " model vdw 2.345 2.170 ... (remaining 97753 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: 2.620 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.050 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.225 10931 Z= 0.670 Angle : 1.531 11.693 15496 Z= 0.957 Chirality : 0.098 0.600 1837 Planarity : 0.011 0.106 1403 Dihedral : 25.464 175.798 5117 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.08 % Favored : 88.65 % Rotamer: Outliers : 20.48 % Allowed : 13.92 % Favored : 65.60 % 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: -3.80 (0.24), residues: 881 helix: -1.84 (0.17), residues: 663 sheet: -4.83 (0.91), residues: 24 loop : -3.99 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP A 33 HIS 0.018 0.004 HIS A 133 PHE 0.057 0.009 PHE A 231 TYR 0.081 0.008 TYR C 28 ARG 0.018 0.002 ARG B 22 *********************** 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 307 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 154 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (ptm-80) REVERT: A 112 ASP cc_start: 0.8266 (m-30) cc_final: 0.7874 (t70) REVERT: A 222 ASP cc_start: 0.7857 (p0) cc_final: 0.7309 (t0) REVERT: A 223 ASP cc_start: 0.8338 (t70) cc_final: 0.7797 (t0) REVERT: B 75 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 90 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6794 (tppt) REVERT: B 108 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: C 14 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5925 (ttt) REVERT: C 90 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6468 (mtpp) REVERT: C 92 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6862 (m170) REVERT: D 15 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5919 (tp) REVERT: D 19 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7240 (mmp80) REVERT: D 64 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: D 122 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4464 (mmp-170) REVERT: E 19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6777 (mmm160) REVERT: E 50 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6861 (mt) REVERT: E 52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6769 (tp40) REVERT: E 54 GLU cc_start: 0.7082 (tt0) cc_final: 0.6832 (tt0) REVERT: E 63 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6125 (t0) REVERT: E 77 MET cc_start: 0.8196 (tpt) cc_final: 0.7620 (tpp) REVERT: E 90 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6491 (ttmm) REVERT: E 94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: F 13 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3437 (mt0) REVERT: F 14 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.3709 (ttp) REVERT: F 19 ARG cc_start: 0.6747 (tpp80) cc_final: 0.6477 (mmm160) REVERT: F 43 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: F 65 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6451 (t) REVERT: F 77 MET cc_start: 0.7380 (tpt) cc_final: 0.6831 (tpt) REVERT: F 90 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4841 (mtpp) REVERT: F 122 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4648 (mtt-85) REVERT: F 123 LYS cc_start: 0.3481 (OUTLIER) cc_final: 0.3246 (mttm) outliers start: 153 outliers final: 45 residues processed: 272 average time/residue: 0.3854 time to fit residues: 129.4203 Evaluate side-chains 194 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 127 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ARG 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 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS C 32 GLN C 64 GLN C 121 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN F 13 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10931 Z= 0.261 Angle : 0.677 8.378 15496 Z= 0.354 Chirality : 0.040 0.301 1837 Planarity : 0.006 0.127 1403 Dihedral : 23.982 176.823 3536 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.58 % Favored : 92.51 % Rotamer: Outliers : 6.96 % Allowed : 19.95 % Favored : 73.09 % 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: -1.28 (0.28), residues: 881 helix: 0.02 (0.19), residues: 665 sheet: -4.49 (0.78), residues: 28 loop : -3.13 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 116 HIS 0.005 0.001 HIS A 121 PHE 0.028 0.002 PHE A 231 TYR 0.016 0.002 TYR C 28 ARG 0.008 0.001 ARG B 122 *********************** 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 205 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8405 (m-40) cc_final: 0.8139 (m110) REVERT: A 112 ASP cc_start: 0.8130 (m-30) cc_final: 0.7919 (t0) REVERT: A 223 ASP cc_start: 0.8099 (t70) cc_final: 0.7725 (t0) REVERT: B 54 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: B 108 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: C 14 MET cc_start: 0.5953 (tpt) cc_final: 0.5613 (ttt) REVERT: C 92 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6871 (m-70) REVERT: D 64 GLN cc_start: 0.5465 (OUTLIER) cc_final: 0.5231 (mt0) REVERT: E 22 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7127 (mtm-85) REVERT: E 108 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8002 (tp30) REVERT: F 13 GLN cc_start: 0.3582 (OUTLIER) cc_final: 0.3083 (tt0) REVERT: F 14 MET cc_start: 0.4232 (mmp) cc_final: 0.3151 (ttm) REVERT: F 19 ARG cc_start: 0.6858 (tpp80) cc_final: 0.6631 (mmm160) REVERT: F 26 TYR cc_start: 0.7507 (t80) cc_final: 0.7180 (t80) REVERT: F 77 MET cc_start: 0.7670 (tpt) cc_final: 0.7185 (tpt) REVERT: F 122 ARG cc_start: 0.4786 (OUTLIER) cc_final: 0.3867 (tmm160) outliers start: 52 outliers final: 20 residues processed: 194 average time/residue: 0.3475 time to fit residues: 85.7857 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 64 GLN 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 85 LEU Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS B 38 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 63 ASN F 92 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 10931 Z= 0.434 Angle : 0.717 10.658 15496 Z= 0.367 Chirality : 0.041 0.222 1837 Planarity : 0.007 0.129 1403 Dihedral : 23.556 178.686 3413 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.72 % Favored : 91.60 % Rotamer: Outliers : 5.49 % Allowed : 21.82 % Favored : 72.69 % 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: -1.07 (0.28), residues: 881 helix: 0.10 (0.20), residues: 664 sheet: -3.51 (0.93), residues: 24 loop : -2.95 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 210 HIS 0.006 0.001 HIS A 121 PHE 0.031 0.003 PHE B 80 TYR 0.018 0.002 TYR F 28 ARG 0.007 0.001 ARG B 122 *********************** 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 174 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8244 (m-30) cc_final: 0.7992 (t70) REVERT: A 223 ASP cc_start: 0.8146 (t70) cc_final: 0.7712 (t70) REVERT: A 256 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7533 (mtp-110) REVERT: C 14 MET cc_start: 0.6120 (tpt) cc_final: 0.5757 (ttt) REVERT: C 47 LYS cc_start: 0.7538 (mttm) cc_final: 0.7283 (mtpt) REVERT: C 92 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7182 (m-70) REVERT: E 22 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7108 (mtt90) REVERT: F 14 MET cc_start: 0.4024 (mmp) cc_final: 0.2823 (ttm) REVERT: F 19 ARG cc_start: 0.6905 (tpp80) cc_final: 0.6689 (mmm160) REVERT: F 52 GLN cc_start: 0.8186 (tp40) cc_final: 0.7924 (tp40) REVERT: F 77 MET cc_start: 0.7532 (tpt) cc_final: 0.7049 (tpt) REVERT: F 111 ARG cc_start: 0.6748 (ttp80) cc_final: 0.6269 (ttm110) REVERT: F 122 ARG cc_start: 0.5230 (OUTLIER) cc_final: 0.4919 (mtt-85) outliers start: 41 outliers final: 24 residues processed: 162 average time/residue: 0.3497 time to fit residues: 72.0054 Evaluate side-chains 153 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS C 13 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10931 Z= 0.226 Angle : 0.609 8.030 15496 Z= 0.311 Chirality : 0.036 0.169 1837 Planarity : 0.006 0.124 1403 Dihedral : 23.099 179.043 3399 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.02 % Favored : 93.42 % Rotamer: Outliers : 5.09 % Allowed : 22.62 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.28), residues: 881 helix: 0.55 (0.20), residues: 665 sheet: -3.44 (0.97), residues: 28 loop : -2.72 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.005 0.001 HIS D 38 PHE 0.022 0.002 PHE B 80 TYR 0.012 0.001 TYR A 107 ARG 0.009 0.000 ARG B 122 *********************** 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 181 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 TYR cc_start: 0.7987 (t80) cc_final: 0.7758 (t80) REVERT: C 14 MET cc_start: 0.6028 (tpt) cc_final: 0.5651 (ttt) REVERT: C 47 LYS cc_start: 0.7567 (mttm) cc_final: 0.7306 (mtpt) REVERT: C 89 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6643 (mm-40) REVERT: D 47 LYS cc_start: 0.8116 (mttm) cc_final: 0.7883 (mttm) REVERT: E 54 GLU cc_start: 0.7208 (tt0) cc_final: 0.6902 (tt0) REVERT: F 14 MET cc_start: 0.4002 (mmp) cc_final: 0.3613 (ttt) REVERT: F 77 MET cc_start: 0.7530 (tpt) cc_final: 0.7076 (tpt) REVERT: F 111 ARG cc_start: 0.6717 (ttp80) cc_final: 0.6260 (ttm110) outliers start: 38 outliers final: 21 residues processed: 167 average time/residue: 0.3418 time to fit residues: 73.2633 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10931 Z= 0.220 Angle : 0.600 8.977 15496 Z= 0.307 Chirality : 0.036 0.217 1837 Planarity : 0.006 0.122 1403 Dihedral : 22.823 177.885 3386 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.13 % Favored : 93.19 % Rotamer: Outliers : 4.28 % Allowed : 24.10 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 881 helix: 0.77 (0.20), residues: 663 sheet: -3.29 (1.04), residues: 28 loop : -2.52 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.005 0.001 HIS C 92 PHE 0.024 0.002 PHE B 80 TYR 0.012 0.001 TYR C 28 ARG 0.010 0.001 ARG B 122 *********************** 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 170 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 TYR cc_start: 0.8073 (t80) cc_final: 0.7618 (t80) REVERT: C 14 MET cc_start: 0.6067 (tpt) cc_final: 0.5665 (ttt) REVERT: C 47 LYS cc_start: 0.7455 (mttm) cc_final: 0.7187 (mtpt) REVERT: C 89 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6696 (mm-40) REVERT: E 26 TYR cc_start: 0.8231 (t80) cc_final: 0.7978 (t80) REVERT: E 54 GLU cc_start: 0.7193 (tt0) cc_final: 0.6881 (tt0) REVERT: F 77 MET cc_start: 0.7505 (tpt) cc_final: 0.7062 (tpt) REVERT: F 111 ARG cc_start: 0.6752 (ttp80) cc_final: 0.6307 (ttm110) outliers start: 32 outliers final: 21 residues processed: 158 average time/residue: 0.3740 time to fit residues: 77.0628 Evaluate side-chains 146 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.0000 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN D 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10931 Z= 0.188 Angle : 0.593 8.726 15496 Z= 0.301 Chirality : 0.035 0.177 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.605 177.701 3383 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.45 % Favored : 93.98 % Rotamer: Outliers : 3.88 % Allowed : 23.16 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.29), residues: 881 helix: 0.89 (0.20), residues: 666 sheet: -2.82 (1.14), residues: 26 loop : -2.41 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.005 0.001 HIS D 38 PHE 0.022 0.002 PHE B 80 TYR 0.016 0.001 TYR F 20 ARG 0.011 0.001 ARG B 122 *********************** 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 169 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7683 (mtt-85) REVERT: A 290 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6677 (m-70) REVERT: B 26 TYR cc_start: 0.7975 (t80) cc_final: 0.7593 (t80) REVERT: C 14 MET cc_start: 0.6089 (tpt) cc_final: 0.5695 (ttt) REVERT: C 47 LYS cc_start: 0.7520 (mttm) cc_final: 0.7258 (mtpt) REVERT: C 89 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6627 (mm-40) REVERT: E 26 TYR cc_start: 0.8214 (t80) cc_final: 0.7979 (t80) REVERT: E 54 GLU cc_start: 0.7157 (tt0) cc_final: 0.6836 (tt0) REVERT: E 85 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7807 (mt) REVERT: F 77 MET cc_start: 0.7468 (tpt) cc_final: 0.7032 (tpt) REVERT: F 111 ARG cc_start: 0.6760 (ttp80) cc_final: 0.6294 (ttm110) outliers start: 29 outliers final: 20 residues processed: 160 average time/residue: 0.3278 time to fit residues: 67.5280 Evaluate side-chains 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10931 Z= 0.248 Angle : 0.614 8.246 15496 Z= 0.313 Chirality : 0.036 0.176 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.510 177.200 3383 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.24 % Favored : 93.19 % Rotamer: Outliers : 3.61 % Allowed : 23.43 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 881 helix: 0.87 (0.20), residues: 663 sheet: -2.86 (1.12), residues: 26 loop : -2.23 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 81 HIS 0.005 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.017 0.001 TYR F 20 ARG 0.011 0.001 ARG B 122 *********************** 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 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8827 (t80) cc_final: 0.8274 (t80) REVERT: A 256 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7811 (mtt-85) REVERT: A 290 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6654 (m-70) REVERT: B 26 TYR cc_start: 0.8118 (t80) cc_final: 0.7723 (t80) REVERT: C 14 MET cc_start: 0.6045 (tpt) cc_final: 0.5706 (ttt) REVERT: C 47 LYS cc_start: 0.7402 (mttm) cc_final: 0.7139 (mtpt) REVERT: C 89 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6656 (mm-40) REVERT: C 108 GLU cc_start: 0.7172 (tp30) cc_final: 0.6493 (mt-10) REVERT: E 26 TYR cc_start: 0.8249 (t80) cc_final: 0.8037 (t80) REVERT: E 50 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6958 (mt) REVERT: E 85 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7765 (mt) REVERT: F 77 MET cc_start: 0.7500 (tpt) cc_final: 0.7034 (tpt) REVERT: F 111 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6351 (ttm110) outliers start: 27 outliers final: 17 residues processed: 147 average time/residue: 0.3237 time to fit residues: 61.4809 Evaluate side-chains 147 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN D 92 HIS F 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10931 Z= 0.241 Angle : 0.609 8.294 15496 Z= 0.309 Chirality : 0.036 0.181 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.405 177.469 3381 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.02 % Favored : 93.42 % Rotamer: Outliers : 3.61 % Allowed : 23.43 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 881 helix: 0.86 (0.19), residues: 667 sheet: -2.89 (1.11), residues: 26 loop : -2.44 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.018 0.001 TYR F 20 ARG 0.013 0.001 ARG B 122 *********************** 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 156 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8844 (t80) cc_final: 0.8327 (t80) REVERT: A 198 ASP cc_start: 0.7952 (t0) cc_final: 0.7721 (t0) REVERT: A 256 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7792 (mtt-85) REVERT: A 290 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6678 (m-70) REVERT: B 26 TYR cc_start: 0.8076 (t80) cc_final: 0.7663 (t80) REVERT: C 14 MET cc_start: 0.6032 (tpt) cc_final: 0.5694 (ttt) REVERT: C 47 LYS cc_start: 0.7508 (mttm) cc_final: 0.7233 (mtpt) REVERT: C 89 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6675 (mm-40) REVERT: C 108 GLU cc_start: 0.7173 (tp30) cc_final: 0.6489 (mt-10) REVERT: E 26 TYR cc_start: 0.8225 (t80) cc_final: 0.8023 (t80) REVERT: E 85 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7751 (mt) REVERT: F 77 MET cc_start: 0.7487 (tpt) cc_final: 0.7031 (tpt) REVERT: F 111 ARG cc_start: 0.6828 (ttp80) cc_final: 0.6365 (ttm110) outliers start: 27 outliers final: 22 residues processed: 145 average time/residue: 0.3378 time to fit residues: 63.8568 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10931 Z= 0.212 Angle : 0.603 9.110 15496 Z= 0.305 Chirality : 0.035 0.186 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.331 178.442 3381 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.79 % Favored : 93.64 % Rotamer: Outliers : 3.61 % Allowed : 23.69 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 881 helix: 0.94 (0.19), residues: 666 sheet: -2.89 (1.10), residues: 26 loop : -2.38 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.020 0.001 TYR F 20 ARG 0.012 0.001 ARG B 122 *********************** 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 152 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8143 (mt) cc_final: 0.7372 (mt) REVERT: A 193 TYR cc_start: 0.8828 (t80) cc_final: 0.8406 (t80) REVERT: A 256 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7706 (mtt-85) REVERT: A 290 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6675 (m-70) REVERT: B 26 TYR cc_start: 0.8031 (t80) cc_final: 0.7602 (t80) REVERT: B 77 MET cc_start: 0.7372 (tpt) cc_final: 0.6827 (tpt) REVERT: C 14 MET cc_start: 0.6028 (tpt) cc_final: 0.5690 (ttt) REVERT: C 47 LYS cc_start: 0.7517 (mttm) cc_final: 0.7241 (mtpt) REVERT: C 89 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6669 (mm-40) REVERT: C 108 GLU cc_start: 0.7152 (tp30) cc_final: 0.6480 (mt-10) REVERT: E 44 MET cc_start: 0.8277 (mtp) cc_final: 0.7996 (mtp) REVERT: E 50 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6964 (mt) REVERT: E 85 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7760 (mt) REVERT: F 77 MET cc_start: 0.7485 (tpt) cc_final: 0.7017 (tpt) REVERT: F 111 ARG cc_start: 0.6861 (ttp80) cc_final: 0.6402 (ttm110) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.3197 time to fit residues: 59.7350 Evaluate side-chains 148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10931 Z= 0.248 Angle : 0.620 9.916 15496 Z= 0.315 Chirality : 0.036 0.187 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.284 178.560 3381 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.24 % Favored : 93.19 % Rotamer: Outliers : 3.48 % Allowed : 23.83 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 881 helix: 0.92 (0.20), residues: 664 sheet: -3.01 (1.08), residues: 26 loop : -2.34 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.020 0.001 TYR F 20 ARG 0.014 0.001 ARG B 122 ********************** 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 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8849 (t80) cc_final: 0.8363 (t80) REVERT: A 256 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7790 (mtt-85) REVERT: A 290 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6603 (m-70) REVERT: B 26 TYR cc_start: 0.8107 (t80) cc_final: 0.7682 (t80) REVERT: C 14 MET cc_start: 0.6027 (tpt) cc_final: 0.5688 (ttt) REVERT: C 47 LYS cc_start: 0.7398 (mttm) cc_final: 0.7128 (mtpt) REVERT: C 89 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6669 (mm-40) REVERT: C 108 GLU cc_start: 0.7174 (tp30) cc_final: 0.6497 (mt-10) REVERT: E 44 MET cc_start: 0.8326 (mtp) cc_final: 0.8042 (mtp) REVERT: E 50 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6991 (mt) REVERT: E 85 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7701 (mt) REVERT: F 111 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6406 (ttm110) outliers start: 26 outliers final: 22 residues processed: 140 average time/residue: 0.3278 time to fit residues: 59.3079 Evaluate side-chains 146 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149838 restraints weight = 12800.765| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.20 r_work: 0.3557 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10931 Z= 0.238 Angle : 0.618 8.998 15496 Z= 0.312 Chirality : 0.036 0.189 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.275 178.888 3381 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.24 % Favored : 93.19 % Rotamer: Outliers : 3.88 % Allowed : 23.69 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 881 helix: 0.94 (0.19), residues: 663 sheet: -3.01 (1.07), residues: 26 loop : -2.28 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.005 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.020 0.001 TYR F 20 ARG 0.014 0.001 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.67 seconds wall clock time: 47 minutes 21.17 seconds (2841.17 seconds total)