Starting phenix.real_space_refine on Thu Jul 2 07:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_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_2026/8djk_27460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.map" model { file = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8djk_27460/07_2026/8djk_27460.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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: 1 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 1.24, per 1000 atoms: 0.17 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: 0.60 Conformation dependent library (CDL) restraints added in 343.8 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: 0.18 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: 1.08 Time building geometry restraints manager: 0.81 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 - 21.71: 3882 21.71 - 43.42: 242 43.42 - 65.13: 51 65.13 - 86.83: 7 86.83 - 108.54: 6 Dihedral angle restraints: 4188 sinusoidal: 1672 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=" CA TRP L 113 " pdb=" C TRP L 113 " pdb=" N PRO L 114 " pdb=" CA PRO L 114 " ideal model delta harmonic sigma weight residual 0.00 22.81 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4185 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 15.273 108.542 2562 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 8.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG C 374 TYR 0.024 0.002 TYR B 174 PHE 0.019 0.002 PHE A 78 TRP 0.010 0.001 TRP L 113 HIS 0.006 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.02880 / 1.50 ( 7266) covalent geometry : angle 1.52362 / 0.87 ( 9914) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 0.58755 / 0.38 ( 4) hydrogen bonds : bond 0.16467 / 10.84 ( 444) hydrogen bonds : angle 6.95863 / 5.11 ( 1278) *********************** 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 : 0.246 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7513 (tpp) cc_final: 0.7030 (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: 0.8391 (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: 0.0910 time to fit residues: 10.5454 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 : 0.266 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4486 r_free = 0.4486 target = 0.219582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172561 restraints weight = 7309.110| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.80 r_work: 0.3635 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7268 Z= 0.165 Angle : 1.408 37.386 9918 Z= 0.520 Chirality : 0.148 2.353 1185 Planarity : 0.004 0.042 1183 Dihedral : 9.240 59.647 1028 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.17 % Allowed : 6.52 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 852 helix: 1.44 (0.22), residues: 527 sheet: -2.46 (0.40), residues: 118 loop : -1.91 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.016 0.001 TYR B 174 PHE 0.020 0.001 PHE A 78 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7266) covalent geometry : angle 1.40814 / 0.52 ( 9914) SS BOND : bond 0.00376 / 0.19 ( 2) SS BOND : angle 0.81224 / 0.58 ( 4) hydrogen bonds : bond 0.04537 / 3.10 ( 444) hydrogen bonds : angle 4.59527 / 3.38 ( 1278) *********************** 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: 16 poor density : 80 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 0.0859 time to fit residues: 10.4949 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 : 0.256 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS C 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.246217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.190159 restraints weight = 8259.344| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.00 r_work: 0.3779 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7268 Z= 0.146 Angle : 1.337 34.642 9918 Z= 0.490 Chirality : 0.147 2.308 1185 Planarity : 0.004 0.042 1183 Dihedral : 8.420 59.496 1026 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.04 % Allowed : 8.42 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 852 helix: 1.80 (0.23), residues: 526 sheet: -1.83 (0.44), residues: 117 loop : -1.74 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.016 0.001 TYR B 174 PHE 0.037 0.001 PHE A 211 TRP 0.004 0.001 TRP L 54 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 7266) covalent geometry : angle 1.33716 / 0.49 ( 9914) SS BOND : bond 0.00285 / 0.14 ( 2) SS BOND : angle 0.75353 / 0.56 ( 4) hydrogen bonds : bond 0.03999 / 2.74 ( 444) hydrogen bonds : angle 4.25676 / 3.12 ( 1278) *********************** 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 95 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8483 (mmp) cc_final: 0.8254 (mpp) REVERT: C 324 MET cc_start: 0.3885 (OUTLIER) cc_final: 0.2921 (tpt) REVERT: L 30 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7576 (mt) REVERT: H 82 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8468 (mtpp) REVERT: H 126 TYR cc_start: 0.9094 (m-80) cc_final: 0.7465 (m-80) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.0752 time to fit residues: 9.2975 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 318 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 76 ASP 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 13 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN C 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.243406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.188402 restraints weight = 8327.140| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 3.47 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7268 Z= 0.190 Angle : 1.346 33.731 9918 Z= 0.498 Chirality : 0.146 2.274 1185 Planarity : 0.004 0.044 1183 Dihedral : 8.416 60.342 1026 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.58 % Allowed : 8.56 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 852 helix: 1.70 (0.23), residues: 527 sheet: -1.52 (0.46), residues: 117 loop : -1.67 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.019 0.002 TYR B 174 PHE 0.038 0.002 PHE A 211 TRP 0.007 0.001 TRP L 54 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 7266) covalent geometry : angle 1.34577 / 0.50 ( 9914) SS BOND : bond 0.00400 / 0.21 ( 2) SS BOND : angle 0.86090 / 0.59 ( 4) hydrogen bonds : bond 0.04519 / 3.11 ( 444) hydrogen bonds : angle 4.31398 / 3.14 ( 1278) *********************** 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 100 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7259 (tt) REVERT: C 324 MET cc_start: 0.3634 (pmm) cc_final: 0.2372 (tpp) REVERT: L 30 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (mt) REVERT: H 126 TYR cc_start: 0.8714 (m-80) cc_final: 0.8148 (m-80) outliers start: 19 outliers final: 12 residues processed: 92 average time/residue: 0.0790 time to fit residues: 10.3409 Evaluate side-chains 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU 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 296 LEU Chi-restraints excluded: chain B residue 318 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.216011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.162241 restraints weight = 7821.441| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.85 r_work: 0.3619 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2599 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= 0.132 Angle : 1.311 32.711 9918 Z= 0.477 Chirality : 0.145 2.217 1185 Planarity : 0.004 0.041 1183 Dihedral : 8.153 60.900 1026 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.31 % Allowed : 10.46 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.30), residues: 852 helix: 1.96 (0.23), residues: 521 sheet: -1.30 (0.48), residues: 117 loop : -1.49 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.016 0.001 TYR H 79 PHE 0.035 0.001 PHE A 211 TRP 0.005 0.001 TRP H 66 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7266) covalent geometry : angle 1.31073 / 0.48 ( 9914) SS BOND : bond 0.00276 / 0.14 ( 2) SS BOND : angle 0.58821 / 0.40 ( 4) hydrogen bonds : bond 0.03724 / 2.56 ( 444) hydrogen bonds : angle 4.10740 / 3.00 ( 1278) *********************** 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 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 ASN cc_start: 0.7627 (t0) cc_final: 0.7389 (m-40) REVERT: B 283 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6936 (tt) REVERT: C 324 MET cc_start: 0.3840 (OUTLIER) cc_final: 0.3045 (tpp) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.0708 time to fit residues: 9.4204 Evaluate side-chains 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 B residue 62 LEU 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 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 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.216121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.162166 restraints weight = 7808.768| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.87 r_work: 0.3615 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7268 Z= 0.133 Angle : 1.311 32.375 9918 Z= 0.478 Chirality : 0.144 2.174 1185 Planarity : 0.004 0.039 1183 Dihedral : 8.019 63.254 1026 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.17 % Allowed : 10.87 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.30), residues: 852 helix: 1.98 (0.23), residues: 526 sheet: -1.19 (0.49), residues: 117 loop : -1.44 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.015 0.001 TYR B 174 PHE 0.016 0.001 PHE A 78 TRP 0.005 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7266) covalent geometry : angle 1.31114 / 0.48 ( 9914) SS BOND : bond 0.00310 / 0.16 ( 2) SS BOND : angle 0.63476 / 0.43 ( 4) hydrogen bonds : bond 0.03727 / 2.57 ( 444) hydrogen bonds : angle 4.05784 / 2.97 ( 1278) *********************** 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 96 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (tt) REVERT: C 324 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.3113 (tpp) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.0684 time to fit residues: 9.0134 Evaluate side-chains 90 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 ASN C 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.218069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164679 restraints weight = 7756.681| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.83 r_work: 0.3629 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2909 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= 0.122 Angle : 1.303 32.137 9918 Z= 0.474 Chirality : 0.144 2.147 1185 Planarity : 0.004 0.040 1183 Dihedral : 7.868 64.175 1026 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.90 % Allowed : 11.55 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.30), residues: 852 helix: 2.02 (0.23), residues: 526 sheet: -1.01 (0.50), residues: 112 loop : -1.30 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.017 0.001 TYR H 79 PHE 0.013 0.001 PHE A 78 TRP 0.006 0.001 TRP H 66 HIS 0.003 0.000 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7266) covalent geometry : angle 1.30320 / 0.47 ( 9914) SS BOND : bond 0.00268 / 0.14 ( 2) SS BOND : angle 0.52298 / 0.37 ( 4) hydrogen bonds : bond 0.03501 / 2.42 ( 444) hydrogen bonds : angle 3.99690 / 2.93 ( 1278) *********************** 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 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6873 (tt) REVERT: C 324 MET cc_start: 0.3871 (OUTLIER) cc_final: 0.3166 (tpp) outliers start: 14 outliers final: 11 residues processed: 86 average time/residue: 0.0680 time to fit residues: 8.4190 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 : 0.249 ------------------------------------------------------------------------------- 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 193 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 LYS 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 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 51 optimal weight: 0.0060 chunk 59 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.227014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167913 restraints weight = 8177.765| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.52 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2923 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= 0.177 Angle : 1.327 32.403 9918 Z= 0.491 Chirality : 0.145 2.159 1185 Planarity : 0.004 0.042 1183 Dihedral : 7.977 63.911 1026 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.17 % Allowed : 12.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.30), residues: 852 helix: 1.85 (0.23), residues: 526 sheet: -0.86 (0.50), residues: 110 loop : -1.29 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.019 0.002 TYR B 174 PHE 0.016 0.001 PHE A 78 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 7266) covalent geometry : angle 1.32765 / 0.49 ( 9914) SS BOND : bond 0.00408 / 0.21 ( 2) SS BOND : angle 0.82393 / 0.55 ( 4) hydrogen bonds : bond 0.04257 / 2.94 ( 444) hydrogen bonds : angle 4.15315 / 3.03 ( 1278) *********************** 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 93 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7110 (tt) REVERT: C 324 MET cc_start: 0.3763 (OUTLIER) cc_final: 0.2612 (tpp) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0710 time to fit residues: 8.8607 Evaluate side-chains 90 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 193 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain L residue 39 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 16 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.229996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.164435 restraints weight = 8053.152| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.30 r_work: 0.3690 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3081 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= 0.127 Angle : 1.310 32.164 9918 Z= 0.480 Chirality : 0.144 2.122 1185 Planarity : 0.004 0.041 1183 Dihedral : 7.776 63.584 1026 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 12.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.30), residues: 852 helix: 1.96 (0.23), residues: 526 sheet: -0.92 (0.50), residues: 112 loop : -1.17 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 118 TYR 0.016 0.001 TYR H 79 PHE 0.042 0.001 PHE A 211 TRP 0.005 0.001 TRP H 66 HIS 0.002 0.000 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7266) covalent geometry : angle 1.31057 / 0.48 ( 9914) SS BOND : bond 0.00297 / 0.15 ( 2) SS BOND : angle 0.56129 / 0.40 ( 4) hydrogen bonds : bond 0.03595 / 2.49 ( 444) hydrogen bonds : angle 4.07142 / 2.98 ( 1278) *********************** 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 : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8582 (tm-30) REVERT: B 283 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6956 (tt) REVERT: C 324 MET cc_start: 0.3818 (OUTLIER) cc_final: 0.3133 (tpp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.0722 time to fit residues: 9.0549 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 29 ILE Chi-restraints excluded: chain L residue 39 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.227043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167807 restraints weight = 8116.358| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.43 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7268 Z= 0.178 Angle : 1.328 32.425 9918 Z= 0.491 Chirality : 0.145 2.144 1185 Planarity : 0.004 0.041 1183 Dihedral : 7.920 63.551 1026 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.31 % Allowed : 12.36 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 852 helix: 1.84 (0.23), residues: 525 sheet: -0.82 (0.50), residues: 110 loop : -1.16 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.019 0.002 TYR B 174 PHE 0.047 0.002 PHE A 211 TRP 0.006 0.001 TRP L 54 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 7266) covalent geometry : angle 1.32846 / 0.49 ( 9914) SS BOND : bond 0.00404 / 0.21 ( 2) SS BOND : angle 0.77467 / 0.54 ( 4) hydrogen bonds : bond 0.04282 / 2.96 ( 444) hydrogen bonds : angle 4.16727 / 3.04 ( 1278) ********************** 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 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 283 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7140 (tt) REVERT: C 324 MET cc_start: 0.3753 (OUTLIER) cc_final: 0.2611 (tpp) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.0724 time to fit residues: 9.1226 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 29 ILE Chi-restraints excluded: chain L residue 39 SER 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 61 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.230344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168705 restraints weight = 8061.544| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.31 r_work: 0.3620 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3179 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= 0.134 Angle : 1.307 32.156 9918 Z= 0.478 Chirality : 0.144 2.112 1185 Planarity : 0.004 0.043 1183 Dihedral : 7.702 63.296 1026 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.04 % Allowed : 12.50 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 852 helix: 1.95 (0.23), residues: 526 sheet: -0.86 (0.50), residues: 112 loop : -1.13 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.014 0.001 TYR B 174 PHE 0.053 0.001 PHE A 211 TRP 0.004 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7266) covalent geometry : angle 1.30736 / 0.48 ( 9914) SS BOND : bond 0.00321 / 0.16 ( 2) SS BOND : angle 0.61637 / 0.43 ( 4) hydrogen bonds : bond 0.03610 / 2.50 ( 444) hydrogen bonds : angle 4.04939 / 2.96 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1703.33 seconds wall clock time: 30 minutes 4.46 seconds (1804.46 seconds total)