Starting phenix.real_space_refine on Tue Aug 4 22:21:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufd_42204/08_2026/8ufd_42204.map" } resolution = 3.26 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= -0.000 sd= 0.055 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 Br 2 7.06 5 P 4 5.49 5 S 40 5.16 5 C 4716 2.51 5 N 1166 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7164 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3472 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Unusual residues: {'PTY': 2, 'WJI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Restraints were copied for chains: B Time building chain proxies: 2.29, per 1000 atoms: 0.32 Number of scatterers: 7164 At special positions: 0 Unit cell: (115.048, 90.62, 72.496, 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) Br 2 34.99 S 40 16.00 P 4 15.00 O 1236 8.00 N 1166 7.00 C 4716 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: 0.67 Conformation dependent library (CDL) restraints added in 505.0 milliseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 48 through 84 removed outlier: 4.382A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 86 through 104 removed outlier: 4.417A pdb=" N ILE A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.764A pdb=" N ASP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 140 through 169 Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 173 through 201 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.769A pdb=" N ILE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 264 Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 267 through 290 removed outlier: 3.927A pdb=" N THR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.640A pdb=" N PHE A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 Processing helix chain 'A' and resid 338 through 365 Proline residue: A 348 - end of helix removed outlier: 4.524A pdb=" N SER A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 401 through 424 removed outlier: 3.540A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.711A pdb=" N VAL A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 4.027A pdb=" N VAL A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 506 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.634A pdb=" N HIS A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 84 removed outlier: 4.382A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 86 through 104 removed outlier: 4.418A pdb=" N ILE B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.764A pdb=" N ASP B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 140 through 169 Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 173 through 201 Processing helix chain 'B' and resid 208 through 211 Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.770A pdb=" N ILE B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 264 Proline residue: B 261 - end of helix Processing helix chain 'B' and resid 267 through 290 removed outlier: 3.928A pdb=" N THR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.641A pdb=" N PHE B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 334 Processing helix chain 'B' and resid 338 through 365 Proline residue: B 348 - end of helix removed outlier: 4.524A pdb=" N SER B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 390 Processing helix chain 'B' and resid 401 through 424 removed outlier: 3.540A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Proline residue: B 418 - end of helix Processing helix chain 'B' and resid 431 through 465 removed outlier: 3.711A pdb=" N VAL B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 4.027A pdb=" N VAL B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 506 Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.633A pdb=" N HIS B 517 " --> pdb=" O GLN B 513 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1788 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: 1.36 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 1135 1.32 - 1.48: 2883 1.48 - 1.63: 3204 1.63 - 1.79: 28 1.79 - 1.94: 56 Bond restraints: 7306 Sorted by residual: bond pdb=" C02 WJI B 603 " pdb=" C04 WJI B 603 " ideal model delta sigma weight residual 1.548 1.340 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C02 WJI A 603 " pdb=" C04 WJI A 603 " ideal model delta sigma weight residual 1.548 1.340 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C30 PTY A 602 " pdb=" O4 PTY A 602 " ideal model delta sigma weight residual 1.331 1.437 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C30 PTY B 602 " pdb=" O4 PTY B 602 " ideal model delta sigma weight residual 1.331 1.436 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C8 PTY B 602 " pdb=" O7 PTY B 602 " ideal model delta sigma weight residual 1.331 1.436 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 7301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 9822 4.45 - 8.89: 84 8.89 - 13.34: 12 13.34 - 17.78: 6 17.78 - 22.23: 4 Bond angle restraints: 9928 Sorted by residual: angle pdb=" C01 WJI A 603 " pdb=" C02 WJI A 603 " pdb=" C04 WJI A 603 " ideal model delta sigma weight residual 110.11 132.34 -22.23 3.00e+00 1.11e-01 5.49e+01 angle pdb=" C01 WJI B 603 " pdb=" C02 WJI B 603 " pdb=" C04 WJI B 603 " ideal model delta sigma weight residual 110.11 132.33 -22.22 3.00e+00 1.11e-01 5.49e+01 angle pdb=" C03 WJI B 603 " pdb=" C02 WJI B 603 " pdb=" C04 WJI B 603 " ideal model delta sigma weight residual 111.50 132.40 -20.90 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C03 WJI A 603 " pdb=" C02 WJI A 603 " pdb=" C04 WJI A 603 " ideal model delta sigma weight residual 111.50 132.39 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O14 PTY B 601 " ideal model delta sigma weight residual 92.90 109.98 -17.08 3.00e+00 1.11e-01 3.24e+01 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.10: 3941 24.10 - 48.19: 247 48.19 - 72.29: 64 72.29 - 96.39: 10 96.39 - 120.48: 4 Dihedral angle restraints: 4266 sinusoidal: 1624 harmonic: 2642 Sorted by residual: dihedral pdb=" CG ARG A 119 " pdb=" CD ARG A 119 " pdb=" NE ARG A 119 " pdb=" CZ ARG A 119 " ideal model delta sinusoidal sigma weight residual -90.00 -4.23 -85.77 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CG ARG B 119 " pdb=" CD ARG B 119 " pdb=" NE ARG B 119 " pdb=" CZ ARG B 119 " ideal model delta sinusoidal sigma weight residual -90.00 -4.23 -85.77 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" N1 PTY B 602 " pdb=" C2 PTY B 602 " pdb=" C3 PTY B 602 " pdb=" O11 PTY B 602 " ideal model delta sinusoidal sigma weight residual 65.33 -174.19 -120.48 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 4263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1083 0.069 - 0.137: 109 0.137 - 0.206: 2 0.206 - 0.275: 0 0.275 - 0.343: 4 Chirality restraints: 1198 Sorted by residual: chirality pdb=" C06 WJI B 603 " pdb=" C05 WJI B 603 " pdb=" C07 WJI B 603 " pdb=" C23 WJI B 603 " both_signs ideal model delta sigma weight residual True 2.37 2.71 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C06 WJI A 603 " pdb=" C05 WJI A 603 " pdb=" C07 WJI A 603 " pdb=" C23 WJI A 603 " both_signs ideal model delta sigma weight residual True 2.37 2.71 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C05 WJI B 603 " pdb=" C04 WJI B 603 " pdb=" C06 WJI B 603 " pdb=" C23 WJI B 603 " both_signs ideal model delta sigma weight residual True 2.46 -2.76 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1195 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 513 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLN B 513 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN B 513 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN B 514 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 513 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C GLN A 513 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN A 513 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 514 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 395 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 396 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.025 5.00e-02 4.00e+02 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1189 2.76 - 3.29: 7454 3.29 - 3.83: 12458 3.83 - 4.36: 13701 4.36 - 4.90: 23973 Nonbonded interactions: 58775 Sorted by model distance: nonbonded pdb=" OG SER B 131 " pdb=" O ALA B 147 " model vdw 2.224 3.040 nonbonded pdb=" OG SER A 131 " pdb=" O ALA A 147 " model vdw 2.225 3.040 nonbonded pdb=" NH2 ARG B 110 " pdb=" O PRO B 294 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG A 110 " pdb=" O PRO A 294 " model vdw 2.244 3.120 nonbonded pdb=" O HIS B 485 " pdb=" OG1 THR B 488 " model vdw 2.394 3.040 ... (remaining 58770 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.430 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.008 0.208 7306 Z= 0.386 Angle : 1.109 22.231 9928 Z= 0.446 Chirality : 0.044 0.343 1198 Planarity : 0.005 0.046 1208 Dihedral : 16.990 120.484 2594 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.10 % Allowed : 1.69 % Favored : 95.21 % 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: 2.19 (0.27), residues: 946 helix: 2.02 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.16 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.023 0.001 TYR B 510 PHE 0.017 0.001 PHE B 183 TRP 0.022 0.001 TRP B 265 HIS 0.001 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.39 ( 7306) covalent geometry : angle 1.10896 / 0.45 ( 9928) hydrogen bonds : bond 0.10368 / 6.90 ( 600) hydrogen bonds : angle 4.99595 / 3.79 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 189 ILE cc_start: 0.7950 (mt) cc_final: 0.7726 (mt) REVERT: B 91 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8271 (t) outliers start: 22 outliers final: 2 residues processed: 173 average time/residue: 0.0789 time to fit residues: 19.0144 Evaluate side-chains 126 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 293 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 431 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140289 restraints weight = 8080.639| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.12 r_work: 0.3552 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7306 Z= 0.146 Angle : 0.640 10.377 9928 Z= 0.307 Chirality : 0.040 0.147 1198 Planarity : 0.005 0.036 1208 Dihedral : 12.015 89.152 1188 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.82 % Allowed : 11.83 % Favored : 85.35 % 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: 2.36 (0.26), residues: 946 helix: 2.08 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.92 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 225 TYR 0.015 0.001 TYR B 97 PHE 0.024 0.001 PHE B 128 TRP 0.006 0.001 TRP B 92 HIS 0.001 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 7306) covalent geometry : angle 0.63957 / 0.31 ( 9928) hydrogen bonds : bond 0.04286 / 2.87 ( 600) hydrogen bonds : angle 4.22731 / 3.20 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.254 Fit side-chains REVERT: A 67 MET cc_start: 0.8293 (tmm) cc_final: 0.8029 (tmm) REVERT: A 189 ILE cc_start: 0.8070 (mt) cc_final: 0.7777 (mt) REVERT: A 320 MET cc_start: 0.7043 (tpt) cc_final: 0.6804 (tpt) REVERT: B 91 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8348 (t) REVERT: B 94 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7193 (tp) REVERT: B 97 TYR cc_start: 0.8655 (t80) cc_final: 0.8273 (t80) REVERT: B 135 CYS cc_start: 0.8476 (t) cc_final: 0.8120 (p) REVERT: B 304 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.5111 (tpp80) REVERT: B 517 HIS cc_start: 0.7647 (m90) cc_final: 0.6909 (m90) outliers start: 20 outliers final: 9 residues processed: 151 average time/residue: 0.0733 time to fit residues: 15.7771 Evaluate side-chains 144 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.0030 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136769 restraints weight = 8062.259| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.03 r_work: 0.3545 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7306 Z= 0.138 Angle : 0.599 10.398 9928 Z= 0.293 Chirality : 0.039 0.137 1198 Planarity : 0.004 0.043 1208 Dihedral : 10.575 78.609 1188 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.38 % Allowed : 13.38 % Favored : 83.24 % 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: 2.47 (0.27), residues: 946 helix: 2.13 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.72 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 225 TYR 0.018 0.001 TYR A 464 PHE 0.014 0.001 PHE B 183 TRP 0.014 0.001 TRP B 92 HIS 0.001 0.000 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7306) covalent geometry : angle 0.59857 / 0.29 ( 9928) hydrogen bonds : bond 0.04186 / 2.81 ( 600) hydrogen bonds : angle 4.11123 / 3.10 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8288 (tmm) cc_final: 0.7892 (tmm) REVERT: A 105 MET cc_start: 0.6401 (ttp) cc_final: 0.6115 (ttp) REVERT: A 189 ILE cc_start: 0.8157 (mt) cc_final: 0.7937 (mt) REVERT: A 320 MET cc_start: 0.7054 (tpt) cc_final: 0.6664 (tpt) REVERT: B 94 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 472 VAL cc_start: 0.7556 (m) cc_final: 0.7184 (t) REVERT: B 517 HIS cc_start: 0.7771 (m90) cc_final: 0.6963 (m90) outliers start: 24 outliers final: 16 residues processed: 161 average time/residue: 0.0755 time to fit residues: 17.2323 Evaluate side-chains 150 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 81 ASN B 431 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130399 restraints weight = 8224.821| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.98 r_work: 0.3468 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7306 Z= 0.174 Angle : 0.628 8.837 9928 Z= 0.312 Chirality : 0.041 0.132 1198 Planarity : 0.004 0.037 1208 Dihedral : 9.929 81.816 1182 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.80 % Allowed : 16.76 % Favored : 79.44 % 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: 2.34 (0.27), residues: 946 helix: 2.08 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -0.83 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 366 TYR 0.015 0.002 TYR B 464 PHE 0.012 0.001 PHE B 183 TRP 0.018 0.001 TRP B 92 HIS 0.002 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 7306) covalent geometry : angle 0.62758 / 0.31 ( 9928) hydrogen bonds : bond 0.04557 / 3.06 ( 600) hydrogen bonds : angle 4.13651 / 3.12 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.6471 (ttt) cc_final: 0.6187 (ttt) REVERT: B 97 TYR cc_start: 0.8725 (t80) cc_final: 0.8299 (t80) REVERT: B 431 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: B 472 VAL cc_start: 0.7669 (m) cc_final: 0.7352 (t) REVERT: B 513 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 27 outliers final: 18 residues processed: 157 average time/residue: 0.0639 time to fit residues: 14.7148 Evaluate side-chains 152 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 431 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132797 restraints weight = 8186.809| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.98 r_work: 0.3503 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7306 Z= 0.138 Angle : 0.593 11.101 9928 Z= 0.290 Chirality : 0.039 0.131 1198 Planarity : 0.004 0.034 1208 Dihedral : 9.378 75.707 1182 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.80 % Allowed : 18.31 % Favored : 77.89 % 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: 2.42 (0.27), residues: 946 helix: 2.12 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.77 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.015 0.001 TYR A 464 PHE 0.026 0.001 PHE A 255 TRP 0.012 0.001 TRP B 92 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7306) covalent geometry : angle 0.59259 / 0.29 ( 9928) hydrogen bonds : bond 0.04234 / 2.86 ( 600) hydrogen bonds : angle 4.06800 / 3.07 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8318 (tmm) cc_final: 0.8067 (tmm) REVERT: A 320 MET cc_start: 0.7127 (tpt) cc_final: 0.6797 (tpt) REVERT: B 431 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: B 462 THR cc_start: 0.9392 (t) cc_final: 0.9190 (t) REVERT: B 472 VAL cc_start: 0.7697 (m) cc_final: 0.7384 (t) REVERT: B 513 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8141 (tm-30) outliers start: 27 outliers final: 21 residues processed: 162 average time/residue: 0.0684 time to fit residues: 16.1280 Evaluate side-chains 159 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 431 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 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 = 0.3927 r_free = 0.3927 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129825 restraints weight = 8229.799| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.97 r_work: 0.3455 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7306 Z= 0.171 Angle : 0.611 7.554 9928 Z= 0.305 Chirality : 0.040 0.135 1198 Planarity : 0.004 0.038 1208 Dihedral : 9.296 67.458 1182 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.51 % Allowed : 19.30 % Favored : 76.20 % 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: 2.43 (0.27), residues: 946 helix: 2.17 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -0.73 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 110 TYR 0.015 0.001 TYR B 464 PHE 0.022 0.001 PHE A 255 TRP 0.018 0.001 TRP B 92 HIS 0.014 0.002 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 7306) covalent geometry : angle 0.61146 / 0.30 ( 9928) hydrogen bonds : bond 0.04384 / 2.96 ( 600) hydrogen bonds : angle 4.08637 / 3.09 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.250 Fit side-chains REVERT: A 67 MET cc_start: 0.8321 (tmm) cc_final: 0.8037 (tmm) REVERT: A 449 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 431 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 472 VAL cc_start: 0.7796 (m) cc_final: 0.7483 (t) outliers start: 32 outliers final: 26 residues processed: 153 average time/residue: 0.0685 time to fit residues: 15.3036 Evaluate side-chains 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** 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 = 0.3955 r_free = 0.3955 target = 0.163354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132389 restraints weight = 8048.711| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.91 r_work: 0.3497 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7306 Z= 0.145 Angle : 0.598 7.484 9928 Z= 0.295 Chirality : 0.039 0.130 1198 Planarity : 0.004 0.035 1208 Dihedral : 8.880 61.214 1182 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.80 % Allowed : 20.85 % Favored : 75.35 % 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: 2.53 (0.27), residues: 946 helix: 2.21 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.015 0.001 TYR A 464 PHE 0.022 0.001 PHE A 255 TRP 0.012 0.001 TRP B 92 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 7306) covalent geometry : angle 0.59784 / 0.30 ( 9928) hydrogen bonds : bond 0.04209 / 2.86 ( 600) hydrogen bonds : angle 4.04164 / 3.06 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.250 Fit side-chains REVERT: A 67 MET cc_start: 0.8376 (tmm) cc_final: 0.8093 (tmm) REVERT: A 320 MET cc_start: 0.7281 (tpt) cc_final: 0.7007 (tpt) REVERT: B 97 TYR cc_start: 0.8777 (t80) cc_final: 0.8390 (t80) REVERT: B 472 VAL cc_start: 0.7820 (m) cc_final: 0.7546 (t) outliers start: 27 outliers final: 21 residues processed: 154 average time/residue: 0.0642 time to fit residues: 14.4370 Evaluate side-chains 154 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** 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 = 0.3945 r_free = 0.3945 target = 0.162250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131101 restraints weight = 8039.956| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.93 r_work: 0.3491 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7306 Z= 0.152 Angle : 0.620 12.178 9928 Z= 0.306 Chirality : 0.040 0.130 1198 Planarity : 0.004 0.037 1208 Dihedral : 8.821 61.491 1182 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.66 % Allowed : 21.55 % Favored : 74.79 % 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: 2.56 (0.27), residues: 946 helix: 2.21 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -0.59 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.016 0.001 TYR A 464 PHE 0.020 0.001 PHE B 183 TRP 0.014 0.001 TRP A 92 HIS 0.015 0.002 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7306) covalent geometry : angle 0.61999 / 0.31 ( 9928) hydrogen bonds : bond 0.04258 / 2.88 ( 600) hydrogen bonds : angle 4.04219 / 3.06 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.266 Fit side-chains REVERT: A 67 MET cc_start: 0.8390 (tmm) cc_final: 0.8097 (tmm) REVERT: A 320 MET cc_start: 0.7341 (tpt) cc_final: 0.7020 (tpt) REVERT: B 97 TYR cc_start: 0.8770 (t80) cc_final: 0.8377 (t80) REVERT: B 180 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 472 VAL cc_start: 0.7845 (m) cc_final: 0.7608 (t) outliers start: 26 outliers final: 24 residues processed: 153 average time/residue: 0.0700 time to fit residues: 15.4483 Evaluate side-chains 163 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132787 restraints weight = 8026.068| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.92 r_work: 0.3516 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7306 Z= 0.137 Angle : 0.611 12.054 9928 Z= 0.300 Chirality : 0.039 0.126 1198 Planarity : 0.004 0.036 1208 Dihedral : 8.587 61.522 1182 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.24 % Allowed : 22.25 % Favored : 74.51 % 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: 2.60 (0.27), residues: 946 helix: 2.25 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -0.61 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.016 0.001 TYR A 464 PHE 0.023 0.001 PHE B 183 TRP 0.017 0.001 TRP A 92 HIS 0.008 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7306) covalent geometry : angle 0.61084 / 0.30 ( 9928) hydrogen bonds : bond 0.04123 / 2.80 ( 600) hydrogen bonds : angle 4.01620 / 3.04 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.251 Fit side-chains REVERT: A 67 MET cc_start: 0.8373 (tmm) cc_final: 0.8094 (tmm) REVERT: B 97 TYR cc_start: 0.8722 (t80) cc_final: 0.8337 (t80) REVERT: B 180 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (m) REVERT: B 472 VAL cc_start: 0.7810 (m) cc_final: 0.7573 (t) outliers start: 23 outliers final: 20 residues processed: 151 average time/residue: 0.0703 time to fit residues: 15.1549 Evaluate side-chains 157 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 93 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.6281 > 50:) overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN B 299 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.162497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131420 restraints weight = 7945.907| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.93 r_work: 0.3492 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7306 Z= 0.147 Angle : 0.617 8.003 9928 Z= 0.302 Chirality : 0.040 0.128 1198 Planarity : 0.004 0.036 1208 Dihedral : 8.401 62.197 1182 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.96 % Allowed : 22.68 % Favored : 74.37 % 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: 2.56 (0.27), residues: 946 helix: 2.21 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -0.60 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 110 TYR 0.016 0.001 TYR B 464 PHE 0.019 0.001 PHE B 183 TRP 0.017 0.001 TRP A 92 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7306) covalent geometry : angle 0.61667 / 0.30 ( 9928) hydrogen bonds : bond 0.04180 / 2.83 ( 600) hydrogen bonds : angle 4.01585 / 3.03 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.165 Fit side-chains REVERT: A 67 MET cc_start: 0.8409 (tmm) cc_final: 0.8148 (tmm) REVERT: A 105 MET cc_start: 0.7248 (ttp) cc_final: 0.6970 (ttp) REVERT: A 251 THR cc_start: 0.9050 (t) cc_final: 0.8848 (t) REVERT: B 67 MET cc_start: 0.8314 (tmm) cc_final: 0.8018 (tmm) REVERT: B 105 MET cc_start: 0.7538 (ttp) cc_final: 0.7285 (ttp) REVERT: B 180 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8349 (m) REVERT: B 431 GLN cc_start: 0.9118 (tp40) cc_final: 0.8545 (tt0) outliers start: 21 outliers final: 18 residues processed: 156 average time/residue: 0.0611 time to fit residues: 13.6871 Evaluate side-chains 155 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 84 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.0980 chunk 82 optimal weight: 0.0980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 431 GLN B 476 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136011 restraints weight = 8016.106| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.92 r_work: 0.3550 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7306 Z= 0.127 Angle : 0.608 7.283 9928 Z= 0.298 Chirality : 0.039 0.122 1198 Planarity : 0.004 0.035 1208 Dihedral : 7.919 62.236 1182 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.11 % Allowed : 24.23 % Favored : 73.66 % 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: 2.70 (0.27), residues: 946 helix: 2.32 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.016 0.001 TYR A 464 PHE 0.023 0.001 PHE B 183 TRP 0.017 0.001 TRP A 92 HIS 0.003 0.000 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 7306) covalent geometry : angle 0.60807 / 0.30 ( 9928) hydrogen bonds : bond 0.03859 / 2.63 ( 600) hydrogen bonds : angle 3.94460 / 2.98 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.99 seconds wall clock time: 33 minutes 6.73 seconds (1986.73 seconds total)