Starting phenix.real_space_refine on Sat May 2 15:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.cif Found real_map, /net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.map" model { file = "/net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23xk_69358/05_2026/23xk_69358.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4484 2.51 5 N 1016 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s 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: 6632 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3297 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'HG0': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.48, per 1000 atoms: 0.37 Number of scatterers: 6632 At special positions: 0 Unit cell: (66.9719, 113.084, 72.4614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1104 8.00 N 1016 7.00 C 4484 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: 0.57 Conformation dependent library (CDL) restraints added in 373.3 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.7% 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 95 through 98 removed outlier: 3.526A pdb=" N HIS A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 99 through 122 removed outlier: 3.839A pdb=" N HIS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.578A pdb=" N LEU A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Proline residue: A 167 - end of helix Processing helix chain 'A' and resid 185 through 214 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 252 through 283 removed outlier: 4.146A pdb=" N HIS A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 322 removed outlier: 3.637A pdb=" N GLY A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.763A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 371 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 372 through 403 Processing helix chain 'A' and resid 410 through 438 removed outlier: 3.521A pdb=" N PHE A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 476 through 506 Proline residue: A 501 - end of helix Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.526A pdb=" N HIS B 98 " --> pdb=" O ASP B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.837A pdb=" N HIS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.579A pdb=" N LEU B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 185 through 214 Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 252 through 283 removed outlier: 4.146A pdb=" N HIS B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 322 removed outlier: 3.637A pdb=" N GLY B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.764A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 372 through 403 Processing helix chain 'B' and resid 410 through 438 removed outlier: 3.520A pdb=" N PHE B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 476 through 506 Proline residue: B 501 - end of helix 518 hydrogen bonds defined for protein. 1554 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: 0.89 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 988 1.31 - 1.44: 1936 1.44 - 1.57: 3846 1.57 - 1.70: 0 1.70 - 1.83: 46 Bond restraints: 6816 Sorted by residual: bond pdb=" C3 HG0 A 901 " pdb=" C7 HG0 A 901 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C3 HG0 B 901 " pdb=" C7 HG0 B 901 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C2 HG0 B 901 " pdb=" C4 HG0 B 901 " ideal model delta sigma weight residual 1.411 1.548 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C2 HG0 A 901 " pdb=" C4 HG0 A 901 " ideal model delta sigma weight residual 1.411 1.547 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C12 HG0 A 901 " pdb=" N3 HG0 A 901 " ideal model delta sigma weight residual 1.375 1.254 0.121 2.00e-02 2.50e+03 3.69e+01 ... (remaining 6811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 9198 3.12 - 6.23: 93 6.23 - 9.35: 5 9.35 - 12.47: 6 12.47 - 15.59: 2 Bond angle restraints: 9304 Sorted by residual: angle pdb=" CD ARG A 180 " pdb=" NE ARG A 180 " pdb=" CZ ARG A 180 " ideal model delta sigma weight residual 124.40 139.99 -15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CD ARG B 180 " pdb=" NE ARG B 180 " pdb=" CZ ARG B 180 " ideal model delta sigma weight residual 124.40 139.96 -15.56 1.40e+00 5.10e-01 1.24e+02 angle pdb=" NE ARG A 180 " pdb=" CZ ARG A 180 " pdb=" NH2 ARG A 180 " ideal model delta sigma weight residual 119.20 111.79 7.41 9.00e-01 1.23e+00 6.78e+01 angle pdb=" NE ARG B 180 " pdb=" CZ ARG B 180 " pdb=" NH2 ARG B 180 " ideal model delta sigma weight residual 119.20 111.83 7.37 9.00e-01 1.23e+00 6.71e+01 angle pdb=" CB ARG B 180 " pdb=" CG ARG B 180 " pdb=" CD ARG B 180 " ideal model delta sigma weight residual 111.30 101.50 9.80 2.30e+00 1.89e-01 1.81e+01 ... (remaining 9299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3328 16.10 - 32.20: 392 32.20 - 48.31: 102 48.31 - 64.41: 38 64.41 - 80.51: 4 Dihedral angle restraints: 3864 sinusoidal: 1456 harmonic: 2408 Sorted by residual: dihedral pdb=" CD ARG A 180 " pdb=" NE ARG A 180 " pdb=" CZ ARG A 180 " pdb=" NH1 ARG A 180 " ideal model delta sinusoidal sigma weight residual 0.00 78.24 -78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CD ARG B 180 " pdb=" NE ARG B 180 " pdb=" CZ ARG B 180 " pdb=" NH1 ARG B 180 " ideal model delta sinusoidal sigma weight residual 0.00 78.24 -78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CA PHE B 89 " pdb=" C PHE B 89 " pdb=" N PRO B 90 " pdb=" CA PRO B 90 " ideal model delta harmonic sigma weight residual -180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 3861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1114 0.151 - 0.302: 2 0.302 - 0.453: 0 0.453 - 0.604: 2 0.604 - 0.755: 2 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CB VAL A 91 " pdb=" CA VAL A 91 " pdb=" CG1 VAL A 91 " pdb=" CG2 VAL A 91 " both_signs ideal model delta sigma weight residual False -2.63 -1.87 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CB VAL B 91 " pdb=" CA VAL B 91 " pdb=" CG1 VAL B 91 " pdb=" CG2 VAL B 91 " both_signs ideal model delta sigma weight residual False -2.63 -1.87 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CB THR A 97 " pdb=" CA THR A 97 " pdb=" OG1 THR A 97 " pdb=" CG2 THR A 97 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 1117 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 180 " -0.498 9.50e-02 1.11e+02 2.38e-01 1.16e+02 pdb=" NE ARG B 180 " 0.088 2.00e-02 2.50e+03 pdb=" CZ ARG B 180 " -0.153 2.00e-02 2.50e+03 pdb=" NH1 ARG B 180 " 0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG B 180 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 180 " -0.498 9.50e-02 1.11e+02 2.38e-01 1.15e+02 pdb=" NE ARG A 180 " 0.088 2.00e-02 2.50e+03 pdb=" CZ ARG A 180 " -0.153 2.00e-02 2.50e+03 pdb=" NH1 ARG A 180 " 0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG A 180 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 339 " -0.032 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 339 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR A 339 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 339 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 339 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 339 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 339 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 339 " -0.004 2.00e-02 2.50e+03 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 60 2.61 - 3.18: 6292 3.18 - 3.75: 9908 3.75 - 4.33: 14141 4.33 - 4.90: 24487 Nonbonded interactions: 54888 Sorted by model distance: nonbonded pdb=" OD1 ASP A 267 " pdb=" N ALA A 268 " model vdw 2.034 3.120 nonbonded pdb=" OD1 ASP B 267 " pdb=" N ALA B 268 " model vdw 2.035 3.120 nonbonded pdb=" O LEU B 264 " pdb=" OD1 ASP B 267 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A 264 " pdb=" OD1 ASP A 267 " model vdw 2.212 3.040 nonbonded pdb=" O ASN B 220 " pdb=" ND2 ASN B 220 " model vdw 2.319 3.120 ... (remaining 54883 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: 1.540 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.009 0.138 6816 Z= 0.407 Angle : 0.859 15.585 9304 Z= 0.474 Chirality : 0.060 0.755 1120 Planarity : 0.011 0.238 1120 Dihedral : 15.802 80.512 2320 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.56 % Allowed : 1.94 % Favored : 97.50 % 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: -0.04 (0.28), residues: 836 helix: 0.79 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -3.10 (0.37), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.159 0.010 ARG B 180 TYR 0.071 0.004 TYR A 339 PHE 0.042 0.003 PHE A 489 TRP 0.007 0.001 TRP A 409 HIS 0.017 0.002 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 6816) covalent geometry : angle 0.85859 ( 9304) hydrogen bonds : bond 0.12953 ( 518) hydrogen bonds : angle 5.69006 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.226 Fit side-chains REVERT: A 208 MET cc_start: 0.7738 (mmm) cc_final: 0.7436 (mmm) REVERT: A 385 MET cc_start: 0.7596 (ttm) cc_final: 0.7389 (ttp) REVERT: B 208 MET cc_start: 0.7822 (mmm) cc_final: 0.7525 (mmm) outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 0.0844 time to fit residues: 8.0236 Evaluate side-chains 56 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 220 ASN A 227 ASN A 275 HIS B 120 HIS B 220 ASN B 227 ASN B 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.151141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128008 restraints weight = 7314.215| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.59 r_work: 0.3249 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6816 Z= 0.186 Angle : 0.660 13.078 9304 Z= 0.347 Chirality : 0.044 0.155 1120 Planarity : 0.005 0.048 1120 Dihedral : 8.027 63.306 910 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.22 % Allowed : 6.81 % Favored : 90.97 % 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: 0.96 (0.29), residues: 836 helix: 1.48 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.52 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.018 0.002 TYR B 274 PHE 0.017 0.002 PHE B 203 TRP 0.007 0.001 TRP B 434 HIS 0.005 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6816) covalent geometry : angle 0.65970 ( 9304) hydrogen bonds : bond 0.06886 ( 518) hydrogen bonds : angle 4.97281 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.228 Fit side-chains REVERT: A 208 MET cc_start: 0.8635 (mmm) cc_final: 0.8255 (mmm) REVERT: A 252 ASN cc_start: 0.7885 (t0) cc_final: 0.7634 (t0) REVERT: A 385 MET cc_start: 0.8170 (ttm) cc_final: 0.7961 (ttp) REVERT: B 208 MET cc_start: 0.8612 (mmm) cc_final: 0.8215 (mmm) outliers start: 16 outliers final: 8 residues processed: 84 average time/residue: 0.0736 time to fit residues: 8.7203 Evaluate side-chains 69 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 376 HIS B 157 GLN B 220 ASN B 376 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122150 restraints weight = 7402.061| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.62 r_work: 0.3180 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6816 Z= 0.195 Angle : 0.631 10.965 9304 Z= 0.335 Chirality : 0.043 0.164 1120 Planarity : 0.005 0.052 1120 Dihedral : 7.795 60.358 910 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.67 % Allowed : 9.72 % Favored : 88.61 % 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: 1.02 (0.29), residues: 836 helix: 1.51 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.53 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 458 TYR 0.012 0.002 TYR A 274 PHE 0.015 0.002 PHE A 203 TRP 0.007 0.001 TRP A 409 HIS 0.005 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6816) covalent geometry : angle 0.63069 ( 9304) hydrogen bonds : bond 0.06888 ( 518) hydrogen bonds : angle 4.94900 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.200 Fit side-chains REVERT: A 208 MET cc_start: 0.8784 (mmm) cc_final: 0.8455 (mmm) REVERT: A 252 ASN cc_start: 0.7931 (t0) cc_final: 0.7661 (t0) REVERT: A 385 MET cc_start: 0.8296 (ttm) cc_final: 0.8036 (ttp) REVERT: B 208 MET cc_start: 0.8775 (mmm) cc_final: 0.8458 (mmm) outliers start: 12 outliers final: 5 residues processed: 88 average time/residue: 0.0682 time to fit residues: 8.3811 Evaluate side-chains 75 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 267 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 376 HIS B 376 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125514 restraints weight = 7467.986| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.64 r_work: 0.3191 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6816 Z= 0.164 Angle : 0.589 12.177 9304 Z= 0.312 Chirality : 0.041 0.147 1120 Planarity : 0.005 0.053 1120 Dihedral : 7.551 63.008 910 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.64 % Allowed : 9.17 % Favored : 88.19 % 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: 1.20 (0.29), residues: 836 helix: 1.64 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.009 0.001 TYR A 274 PHE 0.015 0.001 PHE B 382 TRP 0.006 0.001 TRP A 434 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6816) covalent geometry : angle 0.58945 ( 9304) hydrogen bonds : bond 0.06316 ( 518) hydrogen bonds : angle 4.82783 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.252 Fit side-chains REVERT: A 208 MET cc_start: 0.8817 (mmm) cc_final: 0.8485 (mmm) REVERT: A 252 ASN cc_start: 0.7925 (t0) cc_final: 0.7666 (t0) REVERT: A 267 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.5041 (m-30) REVERT: A 340 MET cc_start: 0.9061 (mtp) cc_final: 0.8769 (mtp) REVERT: A 385 MET cc_start: 0.8366 (ttm) cc_final: 0.8106 (ttp) REVERT: A 386 TRP cc_start: 0.6680 (m-10) cc_final: 0.6322 (t60) REVERT: A 435 PHE cc_start: 0.7659 (t80) cc_final: 0.7326 (t80) REVERT: B 208 MET cc_start: 0.8821 (mmm) cc_final: 0.8435 (mmm) REVERT: B 267 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5137 (m-30) REVERT: B 321 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7285 (ptp90) REVERT: B 386 TRP cc_start: 0.6608 (m-10) cc_final: 0.6299 (t60) REVERT: B 435 PHE cc_start: 0.7701 (t80) cc_final: 0.7462 (t80) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.0684 time to fit residues: 8.8033 Evaluate side-chains 85 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 376 HIS B 376 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123644 restraints weight = 7538.880| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.64 r_work: 0.3201 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6816 Z= 0.164 Angle : 0.580 11.606 9304 Z= 0.307 Chirality : 0.041 0.149 1120 Planarity : 0.005 0.053 1120 Dihedral : 7.390 62.441 910 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.22 % Allowed : 11.25 % Favored : 86.53 % 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: 1.33 (0.29), residues: 836 helix: 1.71 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.37 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.010 0.001 TYR A 274 PHE 0.016 0.001 PHE B 382 TRP 0.005 0.001 TRP B 108 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6816) covalent geometry : angle 0.58047 ( 9304) hydrogen bonds : bond 0.06257 ( 518) hydrogen bonds : angle 4.79814 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.229 Fit side-chains REVERT: A 208 MET cc_start: 0.8796 (mmm) cc_final: 0.8475 (mmm) REVERT: A 243 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7461 (mm) REVERT: A 252 ASN cc_start: 0.7907 (t0) cc_final: 0.7648 (t0) REVERT: A 267 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.4912 (m-30) REVERT: A 340 MET cc_start: 0.9021 (mtp) cc_final: 0.8728 (mtp) REVERT: A 385 MET cc_start: 0.8324 (ttm) cc_final: 0.8062 (ttp) REVERT: A 386 TRP cc_start: 0.6515 (m-10) cc_final: 0.6158 (t60) REVERT: A 435 PHE cc_start: 0.7572 (t80) cc_final: 0.7220 (t80) REVERT: B 208 MET cc_start: 0.8806 (mmm) cc_final: 0.8492 (mmm) REVERT: B 243 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 267 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.4965 (m-30) REVERT: B 321 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7267 (ptp90) REVERT: B 386 TRP cc_start: 0.6451 (m-10) cc_final: 0.6149 (t60) REVERT: B 435 PHE cc_start: 0.7585 (t80) cc_final: 0.7305 (t80) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.0627 time to fit residues: 7.5781 Evaluate side-chains 80 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 16 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127501 restraints weight = 7469.783| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.63 r_work: 0.3245 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6816 Z= 0.139 Angle : 0.540 10.952 9304 Z= 0.286 Chirality : 0.040 0.138 1120 Planarity : 0.004 0.053 1120 Dihedral : 6.975 63.392 910 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.64 % Allowed : 11.67 % Favored : 85.69 % 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: 1.49 (0.29), residues: 836 helix: 1.81 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.56 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR A 274 PHE 0.016 0.001 PHE B 382 TRP 0.007 0.001 TRP B 108 HIS 0.007 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6816) covalent geometry : angle 0.53979 ( 9304) hydrogen bonds : bond 0.05623 ( 518) hydrogen bonds : angle 4.63436 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.252 Fit side-chains REVERT: A 208 MET cc_start: 0.8729 (mmm) cc_final: 0.8390 (mmm) REVERT: A 243 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7390 (mm) REVERT: A 252 ASN cc_start: 0.7887 (t0) cc_final: 0.7629 (t0) REVERT: A 267 ASP cc_start: 0.5729 (OUTLIER) cc_final: 0.4830 (m-30) REVERT: A 385 MET cc_start: 0.8203 (ttm) cc_final: 0.7961 (ttp) REVERT: A 386 TRP cc_start: 0.6488 (m-10) cc_final: 0.6143 (t60) REVERT: A 435 PHE cc_start: 0.7647 (t80) cc_final: 0.7287 (t80) REVERT: B 208 MET cc_start: 0.8734 (mmm) cc_final: 0.8398 (mmm) REVERT: B 243 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7434 (mm) REVERT: B 267 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.4816 (m-30) REVERT: B 386 TRP cc_start: 0.6344 (m-10) cc_final: 0.6070 (t60) REVERT: B 435 PHE cc_start: 0.7683 (t80) cc_final: 0.7333 (t80) outliers start: 19 outliers final: 12 residues processed: 82 average time/residue: 0.0643 time to fit residues: 7.6922 Evaluate side-chains 83 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128222 restraints weight = 7423.559| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.62 r_work: 0.3245 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6816 Z= 0.146 Angle : 0.567 13.098 9304 Z= 0.293 Chirality : 0.040 0.151 1120 Planarity : 0.004 0.052 1120 Dihedral : 6.787 62.180 910 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.08 % Allowed : 12.78 % Favored : 85.14 % 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: 1.55 (0.29), residues: 836 helix: 1.83 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.43 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR A 274 PHE 0.015 0.001 PHE B 382 TRP 0.005 0.001 TRP B 434 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6816) covalent geometry : angle 0.56743 ( 9304) hydrogen bonds : bond 0.05737 ( 518) hydrogen bonds : angle 4.65665 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.233 Fit side-chains REVERT: A 208 MET cc_start: 0.8737 (mmm) cc_final: 0.8408 (mmm) REVERT: A 243 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7450 (mm) REVERT: A 252 ASN cc_start: 0.7848 (t0) cc_final: 0.7596 (t0) REVERT: A 267 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.4594 (m-30) REVERT: A 385 MET cc_start: 0.8323 (ttm) cc_final: 0.8083 (ttp) REVERT: A 386 TRP cc_start: 0.6576 (m-10) cc_final: 0.6219 (t60) REVERT: A 435 PHE cc_start: 0.7638 (t80) cc_final: 0.7271 (t80) REVERT: B 208 MET cc_start: 0.8745 (mmm) cc_final: 0.8420 (mmm) REVERT: B 243 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7477 (mm) REVERT: B 267 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.4778 (m-30) REVERT: B 386 TRP cc_start: 0.6384 (m-10) cc_final: 0.6120 (t60) outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 0.0685 time to fit residues: 8.4364 Evaluate side-chains 81 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125572 restraints weight = 7519.720| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.64 r_work: 0.3212 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6816 Z= 0.166 Angle : 0.589 13.340 9304 Z= 0.305 Chirality : 0.041 0.146 1120 Planarity : 0.004 0.052 1120 Dihedral : 6.814 61.558 910 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.81 % Allowed : 13.75 % Favored : 84.44 % 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: 1.47 (0.29), residues: 836 helix: 1.74 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.33 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.010 0.001 TYR A 274 PHE 0.013 0.001 PHE B 382 TRP 0.005 0.001 TRP A 386 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6816) covalent geometry : angle 0.58891 ( 9304) hydrogen bonds : bond 0.06091 ( 518) hydrogen bonds : angle 4.74170 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.229 Fit side-chains REVERT: A 208 MET cc_start: 0.8784 (mmm) cc_final: 0.8472 (mmm) REVERT: A 243 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7497 (mm) REVERT: A 252 ASN cc_start: 0.7899 (t0) cc_final: 0.7636 (t0) REVERT: A 267 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.4564 (m-30) REVERT: A 385 MET cc_start: 0.8377 (ttm) cc_final: 0.8137 (ttp) REVERT: A 386 TRP cc_start: 0.6619 (m-10) cc_final: 0.6234 (t60) REVERT: A 435 PHE cc_start: 0.7688 (t80) cc_final: 0.7319 (t80) REVERT: B 208 MET cc_start: 0.8790 (mmm) cc_final: 0.8484 (mmm) REVERT: B 243 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7531 (mm) REVERT: B 267 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.4776 (m-30) REVERT: B 386 TRP cc_start: 0.6376 (m-10) cc_final: 0.6097 (t60) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.0664 time to fit residues: 7.7337 Evaluate side-chains 81 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 56 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126477 restraints weight = 7535.754| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.64 r_work: 0.3223 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6816 Z= 0.154 Angle : 0.592 16.052 9304 Z= 0.302 Chirality : 0.041 0.147 1120 Planarity : 0.004 0.052 1120 Dihedral : 6.764 62.114 910 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.08 % Allowed : 13.06 % Favored : 84.86 % 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: 1.52 (0.29), residues: 836 helix: 1.76 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.010 0.001 TYR A 274 PHE 0.013 0.001 PHE B 382 TRP 0.005 0.001 TRP B 386 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6816) covalent geometry : angle 0.59235 ( 9304) hydrogen bonds : bond 0.05902 ( 518) hydrogen bonds : angle 4.71663 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.150 Fit side-chains REVERT: A 243 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7371 (mm) REVERT: A 252 ASN cc_start: 0.7889 (t0) cc_final: 0.7629 (t0) REVERT: A 267 ASP cc_start: 0.5306 (OUTLIER) cc_final: 0.4477 (m-30) REVERT: A 386 TRP cc_start: 0.6589 (m-10) cc_final: 0.6158 (t60) REVERT: A 435 PHE cc_start: 0.7677 (t80) cc_final: 0.7312 (t80) REVERT: B 243 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7397 (mm) REVERT: B 267 ASP cc_start: 0.5220 (OUTLIER) cc_final: 0.4486 (m-30) REVERT: B 386 TRP cc_start: 0.6258 (m-10) cc_final: 0.6048 (t60) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.0719 time to fit residues: 8.3423 Evaluate side-chains 85 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.151910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127449 restraints weight = 7525.301| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.66 r_work: 0.3231 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6816 Z= 0.149 Angle : 0.587 14.920 9304 Z= 0.300 Chirality : 0.040 0.143 1120 Planarity : 0.004 0.052 1120 Dihedral : 6.671 62.101 910 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.81 % Allowed : 13.61 % Favored : 84.58 % 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: 1.58 (0.29), residues: 836 helix: 1.83 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.32 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR A 274 PHE 0.010 0.001 PHE A 335 TRP 0.004 0.001 TRP B 434 HIS 0.007 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6816) covalent geometry : angle 0.58683 ( 9304) hydrogen bonds : bond 0.05749 ( 518) hydrogen bonds : angle 4.69982 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.149 Fit side-chains REVERT: A 243 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7401 (mm) REVERT: A 252 ASN cc_start: 0.7893 (t0) cc_final: 0.7623 (t0) REVERT: A 267 ASP cc_start: 0.5084 (OUTLIER) cc_final: 0.4578 (m-30) REVERT: A 386 TRP cc_start: 0.6435 (m-10) cc_final: 0.6085 (t60) REVERT: B 243 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7384 (mm) REVERT: B 267 ASP cc_start: 0.5080 (OUTLIER) cc_final: 0.4709 (m-30) REVERT: B 386 TRP cc_start: 0.6226 (m-10) cc_final: 0.5966 (t60) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0650 time to fit residues: 7.8736 Evaluate side-chains 84 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125992 restraints weight = 7533.662| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.66 r_work: 0.3215 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6816 Z= 0.161 Angle : 0.601 15.462 9304 Z= 0.307 Chirality : 0.041 0.147 1120 Planarity : 0.004 0.052 1120 Dihedral : 6.704 61.541 910 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.94 % Allowed : 13.33 % Favored : 84.72 % 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: 1.56 (0.29), residues: 836 helix: 1.78 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.21 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.010 0.001 TYR A 274 PHE 0.014 0.001 PHE A 382 TRP 0.004 0.001 TRP B 409 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6816) covalent geometry : angle 0.60110 ( 9304) hydrogen bonds : bond 0.05945 ( 518) hydrogen bonds : angle 4.74218 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.23 seconds wall clock time: 27 minutes 55.94 seconds (1675.94 seconds total)