Starting phenix.real_space_refine on Tue Mar 3 17:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djk_27460/03_2026/8djk_27460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djk_27460/03_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_27460/03_2026/8djk_27460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djk_27460/03_2026/8djk_27460.map" model { file = "/net/cci-nas-00/data/ceres_data/8djk_27460/03_2026/8djk_27460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djk_27460/03_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-5986/lib/python3.9/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 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: 1.66, per 1000 atoms: 0.23 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: 0.66 Conformation dependent library (CDL) restraints added in 262.3 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: 0.21 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: 1.02 Time building geometry restraints manager: 0.86 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: 2.490 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- 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 : 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 covalent geometry : bond 0.02880 ( 7266) covalent geometry : angle 1.52362 ( 9914) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.58755 ( 4) hydrogen bonds : bond 0.16467 ( 444) hydrogen bonds : angle 6.95863 ( 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 : 0.235 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: 0.0884 time to fit residues: 10.2336 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 : 0.245 ------------------------------------------------------------------------------- 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... 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 = 0.4655 r_free = 0.4655 target = 0.240008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.184469 restraints weight = 8138.218| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 3.06 r_work: 0.3708 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7268 Z= 0.164 Angle : 1.411 37.578 9918 Z= 0.520 Chirality : 0.140 2.384 1185 Planarity : 0.005 0.042 1183 Dihedral : 23.762 177.598 1682 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.17 % Allowed : 6.39 % 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 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: 0.08 (0.29), residues: 852 helix: 1.43 (0.23), residues: 527 sheet: -2.47 (0.40), residues: 118 loop : -1.91 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.017 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 covalent geometry : bond 0.00374 ( 7266) covalent geometry : angle 1.41085 ( 9914) SS BOND : bond 0.00381 ( 2) SS BOND : angle 0.83663 ( 4) hydrogen bonds : bond 0.04505 ( 444) hydrogen bonds : angle 4.58938 ( 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 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8446 (tm-30) REVERT: H 39 MET cc_start: 0.8408 (mtm) cc_final: 0.8145 (mtm) outliers start: 16 outliers final: 8 residues processed: 91 average time/residue: 0.0820 time to fit residues: 10.1438 Evaluate side-chains 81 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 B residue 318 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: 0.9990 chunk 57 optimal weight: 30.0000 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 15 optimal weight: 0.6980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 76 GLN C 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.219430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181618 restraints weight = 7382.059| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.47 r_work: 0.3601 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2236 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= 0.155 Angle : 1.347 34.805 9918 Z= 0.495 Chirality : 0.141 2.253 1185 Planarity : 0.004 0.043 1183 Dihedral : 23.187 178.079 1680 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.17 % Allowed : 8.15 % Favored : 89.67 % 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: 0.56 (0.29), residues: 852 helix: 1.72 (0.23), residues: 527 sheet: -1.86 (0.44), residues: 117 loop : -1.74 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.017 0.001 TYR B 174 PHE 0.036 0.001 PHE A 211 TRP 0.005 0.001 TRP L 54 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7266) covalent geometry : angle 1.34739 ( 9914) SS BOND : bond 0.00316 ( 2) SS BOND : angle 0.80572 ( 4) hydrogen bonds : bond 0.04185 ( 444) hydrogen bonds : angle 4.29256 ( 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 97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 324 MET cc_start: 0.3914 (OUTLIER) cc_final: 0.2613 (tpt) REVERT: L 30 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7834 (mt) REVERT: H 126 TYR cc_start: 0.8987 (m-80) cc_final: 0.8616 (m-80) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.0725 time to fit residues: 9.2083 Evaluate side-chains 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 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 = 0.4514 r_free = 0.4514 target = 0.215266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161462 restraints weight = 7804.162| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.05 r_work: 0.3578 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7268 Z= 0.139 Angle : 1.327 33.793 9918 Z= 0.485 Chirality : 0.139 2.151 1185 Planarity : 0.004 0.042 1183 Dihedral : 22.914 176.849 1680 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 9.51 % 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 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: 0.83 (0.29), residues: 852 helix: 1.87 (0.23), residues: 527 sheet: -1.56 (0.46), residues: 118 loop : -1.58 (0.39), residues: 207 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 0.033 0.001 PHE A 211 TRP 0.005 0.001 TRP L 54 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7266) covalent geometry : angle 1.32750 ( 9914) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.65826 ( 4) hydrogen bonds : bond 0.03866 ( 444) hydrogen bonds : angle 4.16120 ( 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 98 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8468 (tm-30) REVERT: B 49 TYR cc_start: 0.6746 (m-10) cc_final: 0.6545 (m-80) REVERT: B 283 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6885 (tt) REVERT: C 324 MET cc_start: 0.3544 (pmm) cc_final: 0.2732 (tpp) REVERT: L 30 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7414 (mt) outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 0.0709 time to fit residues: 9.3348 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 : 0.254 ------------------------------------------------------------------------------- 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 B residue 296 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 76 ASP 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: 0.9980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4539 r_free = 0.4539 target = 0.218073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164618 restraints weight = 7795.658| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.00 r_work: 0.3631 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2751 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= 0.116 Angle : 1.314 33.499 9918 Z= 0.475 Chirality : 0.138 2.103 1185 Planarity : 0.004 0.038 1183 Dihedral : 22.774 176.716 1680 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.04 % Allowed : 10.73 % 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: 1.16 (0.30), residues: 852 helix: 2.07 (0.23), residues: 526 sheet: -1.17 (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 0.016 0.001 TYR H 79 PHE 0.030 0.001 PHE A 211 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.000 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7266) covalent geometry : angle 1.31372 ( 9914) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.53590 ( 4) hydrogen bonds : bond 0.03369 ( 444) hydrogen bonds : angle 3.98835 ( 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 95 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8419 (tm-30) REVERT: B 232 ASN cc_start: 0.7609 (t0) cc_final: 0.7377 (m-40) REVERT: B 283 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6835 (tt) REVERT: C 324 MET cc_start: 0.3844 (OUTLIER) cc_final: 0.3092 (tpp) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.0709 time to fit residues: 9.1536 Evaluate side-chains 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 H residue 21 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.227253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168103 restraints weight = 8134.458| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.32 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2795 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= 0.153 Angle : 1.326 33.373 9918 Z= 0.485 Chirality : 0.139 2.108 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.682 176.921 1678 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.17 % Allowed : 11.28 % 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: 1.13 (0.30), residues: 852 helix: 2.01 (0.23), residues: 521 sheet: -1.09 (0.49), residues: 117 loop : -1.32 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.018 0.002 TYR B 174 PHE 0.035 0.001 PHE A 211 TRP 0.006 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7266) covalent geometry : angle 1.32618 ( 9914) SS BOND : bond 0.00360 ( 2) SS BOND : angle 0.74693 ( 4) hydrogen bonds : bond 0.03976 ( 444) hydrogen bonds : angle 4.07645 ( 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 94 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.7018 (tt) REVERT: C 299 MET cc_start: 0.7780 (mmt) cc_final: 0.7489 (mmt) REVERT: C 324 MET cc_start: 0.3779 (OUTLIER) cc_final: 0.2625 (tpp) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.0670 time to fit residues: 8.6618 Evaluate side-chains 90 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.228443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169548 restraints weight = 8061.119| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.32 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2907 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= 0.138 Angle : 1.322 33.384 9918 Z= 0.481 Chirality : 0.138 2.098 1185 Planarity : 0.004 0.038 1183 Dihedral : 22.661 176.517 1678 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.77 % Allowed : 12.09 % Favored : 86.14 % 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: 2.01 (0.23), residues: 526 sheet: -0.93 (0.49), residues: 117 loop : -1.24 (0.42), residues: 209 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 0.042 0.001 PHE A 211 TRP 0.005 0.001 TRP A 233 HIS 0.002 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7266) covalent geometry : angle 1.32209 ( 9914) SS BOND : bond 0.00318 ( 2) SS BOND : angle 0.62193 ( 4) hydrogen bonds : bond 0.03741 ( 444) hydrogen bonds : angle 4.02144 ( 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: 13 poor density : 78 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6995 (tt) REVERT: C 324 MET cc_start: 0.3735 (OUTLIER) cc_final: 0.2606 (tpp) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.0710 time to fit residues: 8.8280 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 : 0.241 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.226116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159634 restraints weight = 8182.280| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.27 r_work: 0.3596 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7268 Z= 0.185 Angle : 1.342 33.369 9918 Z= 0.495 Chirality : 0.139 2.127 1185 Planarity : 0.004 0.040 1183 Dihedral : 22.691 178.518 1678 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.90 % Allowed : 12.36 % 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: 1.06 (0.30), residues: 852 helix: 1.85 (0.23), residues: 526 sheet: -0.84 (0.49), residues: 115 loop : -1.29 (0.42), residues: 211 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 0.048 0.002 PHE A 211 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7266) covalent geometry : angle 1.34198 ( 9914) SS BOND : bond 0.00422 ( 2) SS BOND : angle 0.77489 ( 4) hydrogen bonds : bond 0.04365 ( 444) hydrogen bonds : angle 4.15796 ( 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 91 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7036 (tt) REVERT: C 324 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3212 (tpp) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.0671 time to fit residues: 8.5803 Evaluate side-chains 87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 39 SER 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 16 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 ASN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.228380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169280 restraints weight = 8065.802| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.36 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3076 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= 0.139 Angle : 1.330 33.455 9918 Z= 0.487 Chirality : 0.138 2.095 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.577 177.022 1678 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % 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: 1.21 (0.30), residues: 852 helix: 1.95 (0.23), residues: 526 sheet: -0.82 (0.51), residues: 112 loop : -1.16 (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 0.051 0.001 PHE A 211 TRP 0.005 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7266) covalent geometry : angle 1.32972 ( 9914) SS BOND : bond 0.00338 ( 2) SS BOND : angle 0.58197 ( 4) hydrogen bonds : bond 0.03802 ( 444) hydrogen bonds : angle 4.07748 ( 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 88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7040 (tt) REVERT: C 324 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.2606 (tpp) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.0697 time to fit residues: 8.2970 Evaluate side-chains 87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 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 298 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.213957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159691 restraints weight = 7854.983| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.46 r_work: 0.3608 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7268 Z= 0.190 Angle : 1.345 33.396 9918 Z= 0.498 Chirality : 0.139 2.133 1185 Planarity : 0.004 0.040 1183 Dihedral : 22.664 178.486 1678 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 12.36 % 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: 1.07 (0.30), residues: 852 helix: 1.81 (0.23), residues: 526 sheet: -0.76 (0.51), residues: 110 loop : -1.21 (0.42), 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 0.055 0.002 PHE A 211 TRP 0.006 0.001 TRP A 233 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7266) covalent geometry : angle 1.34532 ( 9914) SS BOND : bond 0.00442 ( 2) SS BOND : angle 0.75962 ( 4) hydrogen bonds : bond 0.04431 ( 444) hydrogen bonds : angle 4.17970 ( 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 89 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 283 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7088 (tt) REVERT: C 324 MET cc_start: 0.3950 (OUTLIER) cc_final: 0.3225 (tpp) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.0697 time to fit residues: 8.4346 Evaluate side-chains 87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 298 ARG 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 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: 5.9990 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.228122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169114 restraints weight = 8070.311| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.40 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3153 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= 0.143 Angle : 1.324 33.457 9918 Z= 0.484 Chirality : 0.138 2.095 1185 Planarity : 0.004 0.039 1183 Dihedral : 22.547 177.597 1678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.77 % Allowed : 12.23 % 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 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: 1.94 (0.23), residues: 526 sheet: -0.82 (0.51), residues: 112 loop : -1.10 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.015 0.001 TYR B 174 PHE 0.050 0.001 PHE A 211 TRP 0.005 0.001 TRP A 233 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7266) covalent geometry : angle 1.32404 ( 9914) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.62990 ( 4) hydrogen bonds : bond 0.03792 ( 444) hydrogen bonds : angle 4.05902 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.01 seconds wall clock time: 27 minutes 23.41 seconds (1643.41 seconds total)