Starting phenix.real_space_refine on Sat May 2 12:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uur_64516/05_2026/9uur_64516.map" } resolution = 3.36 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= 0.001 sd= 0.173 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 3367 2.51 5 N 903 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5300 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2394 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 288} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 18, 'TRANS': 330} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.64, per 1000 atoms: 0.31 Number of scatterers: 5300 At special positions: 0 Unit cell: (63.5607, 82.9521, 101.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 8 15.00 Mg 1 11.99 O 990 8.00 N 903 7.00 C 3367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 161.2 milliseconds 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 41.2% alpha, 10.0% 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 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.506A pdb=" N ILE A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 162 through 185 removed outlier: 3.743A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.062A pdb=" N MET A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.894A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.902A pdb=" N ILE A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.811A pdb=" N VAL A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 139 through 158 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.993A pdb=" N MET B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.517A pdb=" N ILE B 226 " --> pdb=" O THR B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 249 through 262 removed outlier: 3.621A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.984A pdb=" N ARG B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 4.051A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 296' Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.091A pdb=" N GLU B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.063A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 75 removed outlier: 7.667A pdb=" N ILE A 71 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N SER A 86 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU A 73 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS A 84 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 75 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 81 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 92 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 131 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 198 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.672A pdb=" N GLU B 29 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 47 removed outlier: 4.182A pdb=" N LEU B 45 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER B 58 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 66 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 105 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 128 removed outlier: 3.500A pdb=" N THR B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 540 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: 0.70 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 945 1.32 - 1.45: 1310 1.45 - 1.57: 3097 1.57 - 1.69: 13 1.69 - 1.81: 51 Bond restraints: 5416 Sorted by residual: bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.607 0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" N3B ANP A 501 " pdb=" PG ANP A 501 " ideal model delta sigma weight residual 1.795 1.622 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" O3A ANP A 501 " pdb=" PB ANP A 501 " ideal model delta sigma weight residual 1.700 1.560 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O3P SEP A 218 " pdb=" P SEP A 218 " ideal model delta sigma weight residual 1.610 1.503 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.593 0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 5411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 7180 2.57 - 5.15: 127 5.15 - 7.72: 20 7.72 - 10.29: 6 10.29 - 12.87: 4 Bond angle restraints: 7337 Sorted by residual: angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 113.07 106.87 6.20 1.36e+00 5.41e-01 2.08e+01 angle pdb=" CA GLU B 351 " pdb=" C GLU B 351 " pdb=" O GLU B 351 " ideal model delta sigma weight residual 121.67 117.47 4.20 9.30e-01 1.16e+00 2.04e+01 angle pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " pdb=" O2G ANP B 402 " ideal model delta sigma weight residual 101.05 113.92 -12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 114.46 12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N3B ANP A 501 " pdb=" PG ANP A 501 " pdb=" O2G ANP A 501 " ideal model delta sigma weight residual 101.05 113.11 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 7332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 3088 28.72 - 57.45: 215 57.45 - 86.17: 22 86.17 - 114.89: 3 114.89 - 143.61: 2 Dihedral angle restraints: 3330 sinusoidal: 1416 harmonic: 1914 Sorted by residual: dihedral pdb=" N VAL A 357 " pdb=" C VAL A 357 " pdb=" CA VAL A 357 " pdb=" CB VAL A 357 " ideal model delta harmonic sigma weight residual 123.40 111.62 11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA MET A 187 " pdb=" C MET A 187 " pdb=" N HIS A 188 " pdb=" CA HIS A 188 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" O1A ANP A 501 " pdb=" O3A ANP A 501 " pdb=" PA ANP A 501 " pdb=" PB ANP A 501 " ideal model delta sinusoidal sigma weight residual 83.11 -60.50 143.61 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 3327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 729 0.078 - 0.156: 72 0.156 - 0.234: 4 0.234 - 0.312: 0 0.312 - 0.390: 3 Chirality restraints: 808 Sorted by residual: chirality pdb=" C3' ANP A 501 " pdb=" C2' ANP A 501 " pdb=" C4' ANP A 501 " pdb=" O3' ANP A 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.75 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA VAL A 357 " pdb=" N VAL A 357 " pdb=" C VAL A 357 " pdb=" CB VAL A 357 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 805 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 355 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C LEU A 355 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 355 " -0.018 2.00e-02 2.50e+03 pdb=" N MET A 356 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 189 " 0.193 9.50e-02 1.11e+02 8.64e-02 4.58e+00 pdb=" NE ARG A 189 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 189 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 189 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 189 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 208 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ASP A 208 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 208 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 209 " 0.012 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 16 2.47 - 3.08: 3466 3.08 - 3.69: 7406 3.69 - 4.29: 11012 4.29 - 4.90: 18537 Nonbonded interactions: 40437 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O2B ANP B 402 " model vdw 1.868 2.170 nonbonded pdb=" OD1 ASN B 171 " pdb="MG MG B 401 " model vdw 1.930 2.170 nonbonded pdb=" OD2 ASP B 184 " pdb="MG MG B 401 " model vdw 2.011 2.170 nonbonded pdb=" O LEU B 187 " pdb=" CD1 LEU B 187 " model vdw 2.171 3.460 nonbonded pdb=" ND2 ASN A 195 " pdb=" O1G ANP A 501 " model vdw 2.290 3.120 ... (remaining 40432 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: 0.670 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.007 0.188 5416 Z= 0.410 Angle : 0.840 12.868 7337 Z= 0.433 Chirality : 0.051 0.390 808 Planarity : 0.005 0.086 930 Dihedral : 18.553 143.612 2094 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 20.80 % Favored : 79.20 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.35), residues: 641 helix: 0.84 (0.39), residues: 214 sheet: 0.18 (0.75), residues: 59 loop : -1.20 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.015 0.001 TYR B 47 PHE 0.007 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.002 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 5416) covalent geometry : angle 0.83978 ( 7337) hydrogen bonds : bond 0.17180 ( 188) hydrogen bonds : angle 7.20945 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.203 Fit side-chains REVERT: A 102 GLU cc_start: 0.7769 (mp0) cc_final: 0.7379 (mp0) REVERT: A 134 TYR cc_start: 0.7583 (t80) cc_final: 0.7300 (t80) REVERT: A 138 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7221 (mm-30) REVERT: B 338 ASP cc_start: 0.8192 (t70) cc_final: 0.7813 (t0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0923 time to fit residues: 11.7315 Evaluate side-chains 78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.143236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110015 restraints weight = 6523.824| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.14 r_work: 0.3010 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5416 Z= 0.099 Angle : 0.512 5.970 7337 Z= 0.256 Chirality : 0.041 0.138 808 Planarity : 0.004 0.028 930 Dihedral : 11.890 134.667 781 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.45 % Allowed : 20.28 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.35), residues: 641 helix: 0.93 (0.38), residues: 227 sheet: 0.49 (0.67), residues: 72 loop : -1.17 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.015 0.001 TYR B 47 PHE 0.010 0.001 PHE A 133 TRP 0.008 0.001 TRP A 374 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5416) covalent geometry : angle 0.51225 ( 7337) hydrogen bonds : bond 0.03417 ( 188) hydrogen bonds : angle 5.07841 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.162 Fit side-chains REVERT: A 66 ASP cc_start: 0.8733 (t70) cc_final: 0.8473 (t70) REVERT: A 134 TYR cc_start: 0.7350 (t80) cc_final: 0.7006 (t80) REVERT: A 138 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7104 (mm-30) REVERT: A 233 GLU cc_start: 0.8843 (pm20) cc_final: 0.8602 (pm20) REVERT: B 352 LEU cc_start: 0.8233 (mt) cc_final: 0.7987 (mm) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.0740 time to fit residues: 9.0964 Evaluate side-chains 83 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.141424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109454 restraints weight = 6432.029| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.95 r_work: 0.2999 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5416 Z= 0.116 Angle : 0.506 6.253 7337 Z= 0.254 Chirality : 0.041 0.136 808 Planarity : 0.004 0.031 930 Dihedral : 10.602 132.989 781 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.80 % Allowed : 20.63 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.35), residues: 641 helix: 0.97 (0.37), residues: 234 sheet: 0.40 (0.68), residues: 67 loop : -1.43 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.006 0.001 TYR B 156 PHE 0.008 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.002 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5416) covalent geometry : angle 0.50634 ( 7337) hydrogen bonds : bond 0.03067 ( 188) hydrogen bonds : angle 4.65500 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.181 Fit side-chains REVERT: A 66 ASP cc_start: 0.8715 (t70) cc_final: 0.8458 (t70) REVERT: A 102 GLU cc_start: 0.7829 (mp0) cc_final: 0.7493 (mp0) REVERT: A 107 ILE cc_start: 0.7818 (tt) cc_final: 0.7564 (tt) REVERT: A 134 TYR cc_start: 0.7415 (t80) cc_final: 0.7060 (t80) REVERT: A 138 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7047 (mm-30) REVERT: A 314 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 352 LEU cc_start: 0.8352 (mt) cc_final: 0.8082 (mm) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.0646 time to fit residues: 8.3018 Evaluate side-chains 92 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.151122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118765 restraints weight = 6374.823| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.08 r_work: 0.2989 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5416 Z= 0.113 Angle : 0.495 6.493 7337 Z= 0.249 Chirality : 0.041 0.136 808 Planarity : 0.003 0.032 930 Dihedral : 10.167 132.949 781 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.50 % Allowed : 20.98 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.35), residues: 641 helix: 0.90 (0.37), residues: 240 sheet: 0.50 (0.67), residues: 67 loop : -1.45 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.009 0.001 TYR A 240 PHE 0.008 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5416) covalent geometry : angle 0.49530 ( 7337) hydrogen bonds : bond 0.02914 ( 188) hydrogen bonds : angle 4.46953 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.201 Fit side-chains REVERT: A 66 ASP cc_start: 0.8741 (t70) cc_final: 0.8476 (t70) REVERT: A 107 ILE cc_start: 0.7799 (tt) cc_final: 0.7577 (tt) REVERT: A 134 TYR cc_start: 0.7439 (t80) cc_final: 0.7086 (t80) REVERT: A 138 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7034 (mm-30) REVERT: A 203 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6663 (pt0) REVERT: B 352 LEU cc_start: 0.8457 (mt) cc_final: 0.8216 (mm) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 0.0662 time to fit residues: 8.5089 Evaluate side-chains 88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.0470 chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121059 restraints weight = 6488.679| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.07 r_work: 0.3002 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5416 Z= 0.099 Angle : 0.489 6.773 7337 Z= 0.246 Chirality : 0.040 0.148 808 Planarity : 0.003 0.031 930 Dihedral : 10.027 132.364 781 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.32 % Allowed : 21.68 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.35), residues: 641 helix: 1.05 (0.37), residues: 234 sheet: 0.57 (0.67), residues: 67 loop : -1.39 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.015 0.001 TYR B 47 PHE 0.008 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5416) covalent geometry : angle 0.48911 ( 7337) hydrogen bonds : bond 0.02722 ( 188) hydrogen bonds : angle 4.39006 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.223 Fit side-chains REVERT: A 102 GLU cc_start: 0.7814 (mp0) cc_final: 0.7495 (mp0) REVERT: A 107 ILE cc_start: 0.7865 (tt) cc_final: 0.7635 (tt) REVERT: A 134 TYR cc_start: 0.7432 (t80) cc_final: 0.7090 (t80) REVERT: A 138 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7079 (mm-30) REVERT: A 203 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6654 (pt0) REVERT: A 308 MET cc_start: 0.7488 (mmm) cc_final: 0.7280 (tpt) REVERT: B 352 LEU cc_start: 0.8572 (mt) cc_final: 0.8346 (mm) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 0.0675 time to fit residues: 8.5822 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 23 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.142236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110292 restraints weight = 6482.623| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.97 r_work: 0.3008 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5416 Z= 0.094 Angle : 0.482 5.783 7337 Z= 0.243 Chirality : 0.040 0.148 808 Planarity : 0.003 0.032 930 Dihedral : 9.947 132.378 781 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.32 % Allowed : 21.50 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.35), residues: 641 helix: 0.98 (0.37), residues: 240 sheet: 0.56 (0.67), residues: 67 loop : -1.37 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.008 0.001 TYR B 53 PHE 0.007 0.001 PHE A 337 TRP 0.004 0.001 TRP A 247 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5416) covalent geometry : angle 0.48182 ( 7337) hydrogen bonds : bond 0.02607 ( 188) hydrogen bonds : angle 4.32559 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.145 Fit side-chains REVERT: A 107 ILE cc_start: 0.7821 (tt) cc_final: 0.7603 (tt) REVERT: A 134 TYR cc_start: 0.7377 (t80) cc_final: 0.7048 (t80) REVERT: A 138 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7022 (mm-30) REVERT: A 203 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6570 (pt0) REVERT: B 352 LEU cc_start: 0.8664 (mt) cc_final: 0.8453 (mm) outliers start: 19 outliers final: 18 residues processed: 96 average time/residue: 0.0671 time to fit residues: 8.8147 Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 14 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.139452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107320 restraints weight = 6549.561| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.95 r_work: 0.2971 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5416 Z= 0.146 Angle : 0.534 7.907 7337 Z= 0.267 Chirality : 0.042 0.141 808 Planarity : 0.004 0.033 930 Dihedral : 9.952 132.027 781 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.15 % Allowed : 22.03 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.35), residues: 641 helix: 0.92 (0.37), residues: 240 sheet: 0.64 (0.67), residues: 67 loop : -1.46 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.008 0.001 TYR B 53 PHE 0.011 0.001 PHE A 337 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5416) covalent geometry : angle 0.53371 ( 7337) hydrogen bonds : bond 0.03124 ( 188) hydrogen bonds : angle 4.39273 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.224 Fit side-chains REVERT: A 107 ILE cc_start: 0.7881 (tt) cc_final: 0.7628 (tt) REVERT: A 134 TYR cc_start: 0.7333 (t80) cc_final: 0.7007 (t80) REVERT: A 203 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6612 (pt0) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.0656 time to fit residues: 8.2707 Evaluate side-chains 88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.153508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122277 restraints weight = 6355.659| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.00 r_work: 0.3011 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5416 Z= 0.107 Angle : 0.515 8.402 7337 Z= 0.257 Chirality : 0.041 0.136 808 Planarity : 0.003 0.031 930 Dihedral : 9.861 131.909 781 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.97 % Allowed : 23.08 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.35), residues: 641 helix: 1.00 (0.37), residues: 240 sheet: 0.67 (0.67), residues: 67 loop : -1.41 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.014 0.001 TYR B 47 PHE 0.008 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5416) covalent geometry : angle 0.51454 ( 7337) hydrogen bonds : bond 0.02763 ( 188) hydrogen bonds : angle 4.31122 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.220 Fit side-chains REVERT: A 102 GLU cc_start: 0.7699 (mp0) cc_final: 0.7362 (mp0) REVERT: A 107 ILE cc_start: 0.7899 (tt) cc_final: 0.7674 (tt) REVERT: A 134 TYR cc_start: 0.7418 (t80) cc_final: 0.7106 (t80) REVERT: A 203 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6618 (pt0) REVERT: B 335 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6663 (t0) outliers start: 17 outliers final: 15 residues processed: 89 average time/residue: 0.0679 time to fit residues: 8.2060 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 335 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.150961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119586 restraints weight = 6387.635| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.01 r_work: 0.2986 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5416 Z= 0.116 Angle : 0.523 9.803 7337 Z= 0.260 Chirality : 0.041 0.136 808 Planarity : 0.003 0.031 930 Dihedral : 9.815 131.948 781 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.97 % Allowed : 23.25 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.35), residues: 641 helix: 1.02 (0.37), residues: 240 sheet: 0.59 (0.67), residues: 67 loop : -1.41 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR A 240 PHE 0.008 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5416) covalent geometry : angle 0.52319 ( 7337) hydrogen bonds : bond 0.02811 ( 188) hydrogen bonds : angle 4.30350 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.212 Fit side-chains REVERT: A 102 GLU cc_start: 0.7681 (mp0) cc_final: 0.7406 (mp0) REVERT: A 107 ILE cc_start: 0.7857 (tt) cc_final: 0.7630 (tt) REVERT: A 134 TYR cc_start: 0.7324 (t80) cc_final: 0.7013 (t80) REVERT: A 203 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6537 (pt0) REVERT: B 335 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6621 (t0) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.0669 time to fit residues: 8.2268 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.149491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117500 restraints weight = 6465.614| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.07 r_work: 0.2980 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5416 Z= 0.117 Angle : 0.525 9.688 7337 Z= 0.261 Chirality : 0.041 0.136 808 Planarity : 0.003 0.031 930 Dihedral : 9.768 131.998 781 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.45 % Allowed : 24.30 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.35), residues: 641 helix: 1.05 (0.37), residues: 240 sheet: 0.57 (0.67), residues: 67 loop : -1.39 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE A 337 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5416) covalent geometry : angle 0.52506 ( 7337) hydrogen bonds : bond 0.02805 ( 188) hydrogen bonds : angle 4.29462 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.222 Fit side-chains REVERT: A 102 GLU cc_start: 0.7702 (mp0) cc_final: 0.7426 (mp0) REVERT: A 107 ILE cc_start: 0.7949 (tt) cc_final: 0.7718 (tt) REVERT: A 134 TYR cc_start: 0.7403 (t80) cc_final: 0.7087 (t80) REVERT: A 138 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7144 (mm-30) REVERT: A 203 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6620 (pt0) REVERT: B 335 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6729 (t0) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.0718 time to fit residues: 8.6290 Evaluate side-chains 88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115367 restraints weight = 6543.912| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.13 r_work: 0.2990 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5416 Z= 0.101 Angle : 0.523 10.219 7337 Z= 0.258 Chirality : 0.041 0.134 808 Planarity : 0.003 0.035 930 Dihedral : 9.693 132.348 781 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.10 % Allowed : 24.83 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.35), residues: 641 helix: 1.12 (0.37), residues: 240 sheet: 0.55 (0.67), residues: 67 loop : -1.37 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.010 0.001 TYR B 53 PHE 0.007 0.001 PHE A 337 TRP 0.004 0.001 TRP A 247 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5416) covalent geometry : angle 0.52261 ( 7337) hydrogen bonds : bond 0.02632 ( 188) hydrogen bonds : angle 4.26468 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.94 seconds wall clock time: 22 minutes 23.50 seconds (1343.50 seconds total)