Starting phenix.real_space_refine on Fri Jul 25 13:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.map" model { file = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2025/8djk_27460.cif" } resolution = 3.33 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= 0.003 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4637 2.51 5 N 1123 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7091 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1930 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain breaks: 2 Chain: "B" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2152 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain breaks: 2 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'AJP': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'AJP': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 4.87, per 1000 atoms: 0.69 Number of scatterers: 7091 At special positions: 0 Unit cell: (111.986, 101.04, 103.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1295 8.00 N 1123 7.00 C 4637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 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: 2.17 Conformation dependent library (CDL) restraints added in 869.8 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 66.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 0 through 16 removed outlier: 3.776A pdb=" N ARG A 4 " --> pdb=" O ASP A 0 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 5 " --> pdb=" O LYS A 1 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 35 removed outlier: 3.529A pdb=" N VAL A 20 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 35 " --> pdb=" O MET A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 81 Processing helix chain 'A' and resid 89 through 113 removed outlier: 3.697A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 146 removed outlier: 3.546A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 182 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 187 through 211 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.703A pdb=" N ALA A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 274 removed outlier: 3.580A pdb=" N ARG A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.256A pdb=" N ALA B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 56 through 77 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 80 through 104 Processing helix chain 'B' and resid 105 through 108 removed outlier: 3.953A pdb=" N SER B 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 129 through 153 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.087A pdb=" N TYR B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.501A pdb=" N ASP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.932A pdb=" N VAL B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.666A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 253 through 279 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 280 through 288 removed outlier: 4.261A pdb=" N LEU B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 310 through 330 Processing helix chain 'C' and resid 265 through 285 Processing helix chain 'C' and resid 288 through 308 removed outlier: 3.613A pdb=" N VAL C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.955A pdb=" N GLU C 315 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 350 through 367 Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.063A pdb=" N ARG C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.997A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 25 removed outlier: 3.628A pdb=" N PHE L 90 " --> pdb=" O CYS L 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25 removed outlier: 3.628A pdb=" N PHE L 90 " --> pdb=" O CYS L 42 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP L 89 " --> pdb=" O SER L 86 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER L 86 " --> pdb=" O ASP L 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.786A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.808A pdb=" N GLU H 29 " --> pdb=" O THR H 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.779A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 12 1.20 - 1.40: 2795 1.40 - 1.60: 4326 1.60 - 1.80: 101 1.80 - 2.01: 32 Bond restraints: 7266 Sorted by residual: bond pdb=" C07 AJP B 401 " pdb=" C08 AJP B 401 " ideal model delta sigma weight residual 1.550 2.005 -0.455 2.00e-02 2.50e+03 5.18e+02 bond pdb=" C07 AJP A 406 " pdb=" C08 AJP A 406 " ideal model delta sigma weight residual 1.550 2.003 -0.453 2.00e-02 2.50e+03 5.12e+02 bond pdb=" C01 AJP B 401 " pdb=" C02 AJP B 401 " ideal model delta sigma weight residual 1.521 1.972 -0.451 2.00e-02 2.50e+03 5.09e+02 bond pdb=" C01 AJP A 406 " pdb=" C02 AJP A 406 " ideal model delta sigma weight residual 1.521 1.955 -0.434 2.00e-02 2.50e+03 4.71e+02 bond pdb=" C02 AJP A 406 " pdb=" C03 AJP A 406 " ideal model delta sigma weight residual 1.525 1.101 0.424 2.00e-02 2.50e+03 4.50e+02 ... (remaining 7261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 9611 3.53 - 7.05: 247 7.05 - 10.58: 48 10.58 - 14.10: 3 14.10 - 17.63: 5 Bond angle restraints: 9914 Sorted by residual: angle pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta sigma weight residual 120.25 106.53 13.72 1.35e+00 5.49e-01 1.03e+02 angle pdb=" CA TRP L 113 " pdb=" C TRP L 113 " pdb=" N PRO L 114 " ideal model delta sigma weight residual 118.85 109.55 9.30 9.50e-01 1.11e+00 9.59e+01 angle pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" C SER L 26 " ideal model delta sigma weight residual 109.81 126.67 -16.86 2.21e+00 2.05e-01 5.82e+01 angle pdb=" N TRP L 113 " pdb=" CA TRP L 113 " pdb=" C TRP L 113 " ideal model delta sigma weight residual 109.50 98.46 11.04 1.47e+00 4.63e-01 5.64e+01 angle pdb=" O TRP L 113 " pdb=" C TRP L 113 " pdb=" N PRO L 114 " ideal model delta sigma weight residual 121.28 128.52 -7.24 1.00e+00 1.00e+00 5.23e+01 ... (remaining 9909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 4442 35.72 - 71.45: 213 71.45 - 107.17: 96 107.17 - 142.89: 71 142.89 - 178.62: 20 Dihedral angle restraints: 4842 sinusoidal: 2326 harmonic: 2516 Sorted by residual: dihedral pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta harmonic sigma weight residual 180.00 148.65 31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual 122.80 134.83 -12.03 0 2.50e+00 1.60e-01 2.32e+01 dihedral pdb=" C06 AJP B 401 " pdb=" C07 AJP B 401 " pdb=" C12 AJP B 401 " pdb=" C13 AJP B 401 " ideal model delta sinusoidal sigma weight residual 109.15 -72.23 -178.62 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.156: 1134 1.156 - 2.312: 0 2.312 - 3.468: 0 3.468 - 4.624: 7 4.624 - 5.780: 44 Chirality restraints: 1185 Sorted by residual: chirality pdb=" C20 AJP B 401 " pdb=" C15 AJP B 401 " pdb=" C19 AJP B 401 " pdb=" C21 AJP B 401 " both_signs ideal model delta sigma weight residual False 2.96 -2.83 5.78 2.00e-01 2.50e+01 8.35e+02 chirality pdb=" C20 AJP A 406 " pdb=" C15 AJP A 406 " pdb=" C19 AJP A 406 " pdb=" C21 AJP A 406 " both_signs ideal model delta sigma weight residual False 2.96 -2.78 5.73 2.00e-01 2.50e+01 8.21e+02 chirality pdb=" C16 AJP B 401 " pdb=" C11 AJP B 401 " pdb=" C15 AJP B 401 " pdb=" C17 AJP B 401 " both_signs ideal model delta sigma weight residual False -2.70 2.77 -5.47 2.00e-01 2.50e+01 7.48e+02 ... (remaining 1182 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 113 " 0.023 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C TRP L 113 " -0.083 2.00e-02 2.50e+03 pdb=" O TRP L 113 " 0.033 2.00e-02 2.50e+03 pdb=" N PRO L 114 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 113 " -0.076 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO L 114 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 380 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C GLN C 380 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN C 380 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 381 " 0.013 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 220 2.76 - 3.47: 10344 3.47 - 4.19: 15390 4.19 - 4.90: 28893 Nonbonded interactions: 54848 Sorted by model distance: nonbonded pdb=" N PRO B 309 " pdb=" O VAL C 383 " model vdw 1.327 3.120 nonbonded pdb=" CD PRO B 309 " pdb=" O VAL C 383 " model vdw 2.286 3.440 nonbonded pdb=" CA PRO B 309 " pdb=" O VAL C 383 " model vdw 2.296 3.470 nonbonded pdb=" O GLY A 180 " pdb=" OG1 THR A 183 " model vdw 2.346 3.040 nonbonded pdb=" N PRO B 309 " pdb=" C VAL C 383 " model vdw 2.371 3.350 ... (remaining 54843 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 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: 3.470 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.350 Find NCS groups from input model: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.029 0.455 7268 Z= 1.499 Angle : 1.523 17.631 9918 Z= 0.865 Chirality : 1.033 5.780 1185 Planarity : 0.005 0.118 1183 Dihedral : 32.028 178.617 3216 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.82 % Allowed : 4.35 % Favored : 94.84 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.84 (0.26), residues: 852 helix: -0.12 (0.20), residues: 520 sheet: -3.05 (0.39), residues: 117 loop : -2.55 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 113 HIS 0.006 0.001 HIS A 237 PHE 0.019 0.002 PHE A 78 TYR 0.024 0.002 TYR B 174 ARG 0.005 0.001 ARG C 374 Details of bonding type rmsd hydrogen bonds : bond 0.16467 ( 444) hydrogen bonds : angle 6.95863 ( 1278) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.58755 ( 4) covalent geometry : bond 0.02880 ( 7266) covalent geometry : angle 1.52362 ( 9914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7513 (tpp) cc_final: 0.7032 (tpp) REVERT: A 193 MET cc_start: 0.7285 (ttm) cc_final: 0.6903 (ttp) REVERT: B 49 TYR cc_start: 0.6212 (m-10) cc_final: 0.5708 (m-10) REVERT: B 156 LYS cc_start: 0.6992 (mtpt) cc_final: 0.6669 (mtpt) REVERT: B 232 ASN cc_start: 0.6806 (t0) cc_final: 0.6476 (t0) REVERT: H 22 GLN cc_start: 0.7404 (pt0) cc_final: 0.6994 (pt0) REVERT: H 79 TYR cc_start: 0.8706 (m-80) cc_final: 0.8390 (m-80) REVERT: H 81 GLN cc_start: 0.6797 (mp10) cc_final: 0.6582 (mp10) REVERT: H 82 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7808 (ttmt) outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.2087 time to fit residues: 24.0289 Evaluate side-chains 72 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 112 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 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 156 ASN B 95 HIS C 291 GLN L 25 GLN L 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.241695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.185946 restraints weight = 8066.099| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.03 r_work: 0.3724 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7268 Z= 0.156 Angle : 1.407 37.440 9918 Z= 0.518 Chirality : 0.141 2.385 1185 Planarity : 0.004 0.042 1183 Dihedral : 23.711 179.357 1682 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 6.52 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 852 helix: 1.48 (0.23), residues: 527 sheet: -2.47 (0.40), residues: 118 loop : -1.90 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.003 0.001 HIS B 230 PHE 0.020 0.001 PHE A 78 TYR 0.016 0.001 TYR B 174 ARG 0.003 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 444) hydrogen bonds : angle 4.56324 ( 1278) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.76900 ( 4) covalent geometry : bond 0.00350 ( 7266) covalent geometry : angle 1.40718 ( 9914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 39 MET cc_start: 0.8387 (mtm) cc_final: 0.8122 (mtm) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 0.2015 time to fit residues: 24.8460 Evaluate side-chains 80 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 95 HIS B 99 ASN B 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.219192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164968 restraints weight = 7693.669| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.00 r_work: 0.3646 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7268 Z= 0.119 Angle : 1.328 34.625 9918 Z= 0.483 Chirality : 0.139 2.194 1185 Planarity : 0.004 0.039 1183 Dihedral : 23.131 176.276 1680 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.49 % Allowed : 7.88 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.29), residues: 852 helix: 1.98 (0.23), residues: 526 sheet: -1.83 (0.43), residues: 117 loop : -1.67 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 66 HIS 0.002 0.001 HIS B 230 PHE 0.031 0.001 PHE A 211 TYR 0.011 0.001 TYR B 174 ARG 0.002 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 444) hydrogen bonds : angle 4.13304 ( 1278) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.60797 ( 4) covalent geometry : bond 0.00252 ( 7266) covalent geometry : angle 1.32863 ( 9914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8083 (tpp) cc_final: 0.7684 (tpp) REVERT: C 324 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.2956 (tpt) REVERT: L 30 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7513 (mt) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.2331 time to fit residues: 28.5811 Evaluate side-chains 85 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.233571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.174207 restraints weight = 8239.605| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.64 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7268 Z= 0.128 Angle : 1.323 33.822 9918 Z= 0.481 Chirality : 0.139 2.143 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.866 176.542 1680 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.31 % Allowed : 9.24 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.03 (0.29), residues: 852 helix: 2.02 (0.23), residues: 526 sheet: -1.36 (0.46), residues: 118 loop : -1.56 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 PHE 0.029 0.001 PHE A 211 TYR 0.015 0.001 TYR B 174 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 444) hydrogen bonds : angle 4.07751 ( 1278) SS BOND : bond 0.00296 ( 2) SS BOND : angle 0.73390 ( 4) covalent geometry : bond 0.00294 ( 7266) covalent geometry : angle 1.32309 ( 9914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8505 (mt) cc_final: 0.8286 (mt) REVERT: B 50 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 283 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6949 (tt) REVERT: C 324 MET cc_start: 0.3717 (pmm) cc_final: 0.2517 (tpp) REVERT: L 30 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7763 (mt) REVERT: L 98 GLU cc_start: 0.8247 (mp0) cc_final: 0.8026 (mp0) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.1786 time to fit residues: 22.5716 Evaluate side-chains 92 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.233612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174303 restraints weight = 8103.915| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.49 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7268 Z= 0.128 Angle : 1.317 33.411 9918 Z= 0.477 Chirality : 0.138 2.111 1185 Planarity : 0.004 0.038 1183 Dihedral : 22.833 176.293 1680 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.90 % Allowed : 10.33 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.18 (0.30), residues: 852 helix: 2.07 (0.23), residues: 526 sheet: -1.03 (0.49), residues: 117 loop : -1.49 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.003 0.000 HIS B 230 PHE 0.032 0.001 PHE A 211 TYR 0.015 0.001 TYR B 174 ARG 0.002 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 444) hydrogen bonds : angle 4.02302 ( 1278) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.61749 ( 4) covalent geometry : bond 0.00295 ( 7266) covalent geometry : angle 1.31721 ( 9914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: B 50 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 283 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6934 (tt) REVERT: C 324 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.2551 (tpp) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2042 time to fit residues: 24.8803 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 40.0000 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 95 HIS B 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.226288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167823 restraints weight = 8086.424| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.27 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7268 Z= 0.160 Angle : 1.328 33.343 9918 Z= 0.486 Chirality : 0.139 2.119 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.817 177.216 1678 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.45 % Allowed : 10.46 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.13 (0.30), residues: 852 helix: 1.99 (0.23), residues: 526 sheet: -0.95 (0.50), residues: 118 loop : -1.45 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 PHE 0.042 0.001 PHE A 211 TYR 0.020 0.002 TYR B 174 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 444) hydrogen bonds : angle 4.10979 ( 1278) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.69551 ( 4) covalent geometry : bond 0.00389 ( 7266) covalent geometry : angle 1.32840 ( 9914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: B 50 VAL cc_start: 0.8477 (p) cc_final: 0.8188 (p) REVERT: B 283 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7027 (tt) REVERT: C 324 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.2550 (tpp) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 0.1612 time to fit residues: 21.2835 Evaluate side-chains 87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.228036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.163354 restraints weight = 8022.572| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.36 r_work: 0.3625 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7268 Z= 0.148 Angle : 1.324 33.397 9918 Z= 0.483 Chirality : 0.138 2.105 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.706 176.972 1678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.31 % Allowed : 11.01 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.16 (0.30), residues: 852 helix: 1.93 (0.23), residues: 532 sheet: -0.85 (0.50), residues: 117 loop : -1.33 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 PHE 0.043 0.001 PHE A 211 TYR 0.017 0.001 TYR H 79 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 444) hydrogen bonds : angle 4.06983 ( 1278) SS BOND : bond 0.00421 ( 2) SS BOND : angle 0.72711 ( 4) covalent geometry : bond 0.00354 ( 7266) covalent geometry : angle 1.32429 ( 9914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: B 50 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 283 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6955 (tt) REVERT: C 324 MET cc_start: 0.3844 (OUTLIER) cc_final: 0.3145 (tpp) REVERT: H 82 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8440 (ttmt) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.1602 time to fit residues: 20.1360 Evaluate side-chains 90 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.228889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.169981 restraints weight = 8048.791| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.34 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7268 Z= 0.137 Angle : 1.321 33.320 9918 Z= 0.482 Chirality : 0.138 2.096 1185 Planarity : 0.004 0.038 1183 Dihedral : 22.605 177.243 1678 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.31 % Allowed : 11.96 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.24 (0.30), residues: 852 helix: 2.02 (0.23), residues: 526 sheet: -0.76 (0.51), residues: 112 loop : -1.30 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 PHE 0.042 0.001 PHE A 211 TYR 0.017 0.001 TYR H 79 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 444) hydrogen bonds : angle 4.03936 ( 1278) SS BOND : bond 0.00453 ( 2) SS BOND : angle 0.80778 ( 4) covalent geometry : bond 0.00322 ( 7266) covalent geometry : angle 1.32087 ( 9914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: B 50 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 283 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6986 (tt) REVERT: B 299 GLN cc_start: 0.7935 (tp40) cc_final: 0.6612 (tm-30) REVERT: C 324 MET cc_start: 0.3623 (OUTLIER) cc_final: 0.2587 (tpp) REVERT: H 82 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8483 (ttmt) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.2048 time to fit residues: 25.3692 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.227747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168695 restraints weight = 8108.682| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.32 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7268 Z= 0.151 Angle : 1.327 33.299 9918 Z= 0.486 Chirality : 0.138 2.095 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.556 177.650 1678 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.17 % Allowed : 11.82 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.22 (0.30), residues: 852 helix: 1.94 (0.23), residues: 532 sheet: -0.75 (0.51), residues: 112 loop : -1.24 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 PHE 0.044 0.001 PHE A 211 TYR 0.017 0.001 TYR B 174 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 444) hydrogen bonds : angle 4.06740 ( 1278) SS BOND : bond 0.00456 ( 2) SS BOND : angle 0.77712 ( 4) covalent geometry : bond 0.00363 ( 7266) covalent geometry : angle 1.32711 ( 9914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 50 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8165 (p) REVERT: B 283 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7032 (tt) REVERT: C 324 MET cc_start: 0.3646 (OUTLIER) cc_final: 0.2607 (tpp) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.1696 time to fit residues: 20.9597 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 chunk 22 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.231506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.172844 restraints weight = 8245.368| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.82 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7268 Z= 0.121 Angle : 1.313 33.304 9918 Z= 0.477 Chirality : 0.138 2.076 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.442 178.101 1678 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 12.77 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.40 (0.30), residues: 852 helix: 2.11 (0.23), residues: 526 sheet: -0.67 (0.51), residues: 112 loop : -1.18 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 56 HIS 0.002 0.000 HIS B 230 PHE 0.037 0.001 PHE A 211 TYR 0.014 0.001 TYR H 79 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 444) hydrogen bonds : angle 3.98057 ( 1278) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.62737 ( 4) covalent geometry : bond 0.00277 ( 7266) covalent geometry : angle 1.31367 ( 9914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: -0.0109 (mtt) cc_final: -0.0947 (ppp) REVERT: B 50 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 283 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6950 (tt) REVERT: C 324 MET cc_start: 0.3790 (OUTLIER) cc_final: 0.2763 (tpp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.1711 time to fit residues: 20.5245 Evaluate side-chains 85 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.222155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163245 restraints weight = 8156.851| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.47 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 7268 Z= 0.286 Angle : 1.394 33.541 9918 Z= 0.528 Chirality : 0.140 2.171 1185 Planarity : 0.004 0.040 1183 Dihedral : 22.762 179.304 1678 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.04 % Allowed : 12.36 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.73 (0.29), residues: 852 helix: 1.48 (0.22), residues: 533 sheet: -0.81 (0.49), residues: 115 loop : -1.33 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 54 HIS 0.008 0.002 HIS H 99 PHE 0.054 0.002 PHE A 211 TYR 0.023 0.002 TYR B 174 ARG 0.005 0.001 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 444) hydrogen bonds : angle 4.38375 ( 1278) SS BOND : bond 0.00631 ( 2) SS BOND : angle 1.19893 ( 4) covalent geometry : bond 0.00719 ( 7266) covalent geometry : angle 1.39398 ( 9914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.04 seconds wall clock time: 59 minutes 32.86 seconds (3572.86 seconds total)