Starting phenix.real_space_refine on Fri Jun 13 16:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.map" model { file = "/net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gel_29974/06_2025/8gel_29974.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 52 5.16 5 C 9824 2.51 5 N 2620 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15556 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3889 Classifications: {'peptide': 498} Link IDs: {'TRANS': 497} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 8.39, per 1000 atoms: 0.54 Number of scatterers: 15556 At special positions: 0 Unit cell: (127.875, 127.875, 90.75, 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 52 16.00 O 3060 8.00 N 2620 7.00 C 9824 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 96.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 43 removed outlier: 3.847A pdb=" N GLU A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 89 removed outlier: 4.183A pdb=" N ASN A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 131 removed outlier: 3.727A pdb=" N ILE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 170 Processing helix chain 'A' and resid 173 through 210 removed outlier: 3.815A pdb=" N ARG A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 214 through 253 Processing helix chain 'A' and resid 256 through 294 removed outlier: 4.510A pdb=" N GLU A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 335 Processing helix chain 'A' and resid 338 through 375 Processing helix chain 'A' and resid 378 through 422 removed outlier: 3.601A pdb=" N VAL A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 464 Processing helix chain 'A' and resid 466 through 500 Processing helix chain 'B' and resid 2 through 43 removed outlier: 3.848A pdb=" N GLU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 89 removed outlier: 4.183A pdb=" N ASN B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 131 removed outlier: 3.728A pdb=" N ILE B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 170 Processing helix chain 'B' and resid 173 through 210 removed outlier: 3.815A pdb=" N ARG B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 214 through 253 Processing helix chain 'B' and resid 256 through 294 removed outlier: 4.510A pdb=" N GLU B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 335 Processing helix chain 'B' and resid 338 through 375 Processing helix chain 'B' and resid 378 through 422 removed outlier: 3.601A pdb=" N VAL B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 464 Processing helix chain 'B' and resid 466 through 500 Processing helix chain 'C' and resid 2 through 43 removed outlier: 3.847A pdb=" N GLU C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 4.183A pdb=" N ASN C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 131 removed outlier: 3.727A pdb=" N ILE C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 170 Processing helix chain 'C' and resid 173 through 210 removed outlier: 3.815A pdb=" N ARG C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 214 through 253 Processing helix chain 'C' and resid 256 through 294 removed outlier: 4.510A pdb=" N GLU C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 335 Processing helix chain 'C' and resid 338 through 375 Processing helix chain 'C' and resid 378 through 422 removed outlier: 3.602A pdb=" N VAL C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 464 Processing helix chain 'C' and resid 466 through 500 Processing helix chain 'D' and resid 2 through 43 removed outlier: 3.848A pdb=" N GLU D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 89 removed outlier: 4.182A pdb=" N ASN D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 131 removed outlier: 3.726A pdb=" N ILE D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 170 Processing helix chain 'D' and resid 173 through 210 removed outlier: 3.815A pdb=" N ARG D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 214 through 253 Processing helix chain 'D' and resid 256 through 294 removed outlier: 4.510A pdb=" N GLU D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 335 Processing helix chain 'D' and resid 338 through 375 Processing helix chain 'D' and resid 378 through 422 removed outlier: 3.601A pdb=" N VAL D 382 " --> pdb=" O ASP D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 464 Processing helix chain 'D' and resid 466 through 500 1677 hydrogen bonds defined for protein. 5031 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: 5.13 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5396 1.34 - 1.46: 713 1.46 - 1.57: 9387 1.57 - 1.69: 0 1.69 - 1.80: 104 Bond restraints: 15600 Sorted by residual: bond pdb=" CG1 ILE D 18 " pdb=" CD1 ILE D 18 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.14e+00 bond pdb=" CG1 ILE B 18 " pdb=" CD1 ILE B 18 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" CG1 ILE A 18 " pdb=" CD1 ILE A 18 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.08e+00 bond pdb=" CG1 ILE C 18 " pdb=" CD1 ILE C 18 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" CG1 ILE C 7 " pdb=" CD1 ILE C 7 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.98e+00 ... (remaining 15595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 20396 2.19 - 4.37: 356 4.37 - 6.56: 104 6.56 - 8.75: 36 8.75 - 10.93: 12 Bond angle restraints: 20904 Sorted by residual: angle pdb=" N GLU A 130 " pdb=" CA GLU A 130 " pdb=" C GLU A 130 " ideal model delta sigma weight residual 111.82 106.40 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" N GLU B 130 " pdb=" CA GLU B 130 " pdb=" C GLU B 130 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N GLU C 130 " pdb=" CA GLU C 130 " pdb=" C GLU C 130 " ideal model delta sigma weight residual 111.82 106.45 5.37 1.16e+00 7.43e-01 2.14e+01 angle pdb=" N GLU D 130 " pdb=" CA GLU D 130 " pdb=" C GLU D 130 " ideal model delta sigma weight residual 111.82 106.45 5.37 1.16e+00 7.43e-01 2.14e+01 angle pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 109.52 115.76 -6.24 1.55e+00 4.16e-01 1.62e+01 ... (remaining 20899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 8969 17.58 - 35.17: 899 35.17 - 52.75: 168 52.75 - 70.33: 24 70.33 - 87.91: 20 Dihedral angle restraints: 10080 sinusoidal: 4172 harmonic: 5908 Sorted by residual: dihedral pdb=" CA LEU A 334 " pdb=" C LEU A 334 " pdb=" N ALA A 335 " pdb=" CA ALA A 335 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU B 334 " pdb=" C LEU B 334 " pdb=" N ALA B 335 " pdb=" CA ALA B 335 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU D 334 " pdb=" C LEU D 334 " pdb=" N ALA D 335 " pdb=" CA ALA D 335 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2416 0.075 - 0.150: 156 0.150 - 0.225: 12 0.225 - 0.300: 0 0.300 - 0.375: 4 Chirality restraints: 2588 Sorted by residual: chirality pdb=" CB ILE C 307 " pdb=" CA ILE C 307 " pdb=" CG1 ILE C 307 " pdb=" CG2 ILE C 307 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE D 307 " pdb=" CA ILE D 307 " pdb=" CG1 ILE D 307 " pdb=" CG2 ILE D 307 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CB ILE A 307 " pdb=" CA ILE A 307 " pdb=" CG1 ILE A 307 " pdb=" CG2 ILE A 307 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 2585 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ILE A 210 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 210 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 211 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 210 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ILE C 210 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE C 210 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 211 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 210 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C ILE D 210 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE D 210 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS D 211 " 0.014 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 161 2.66 - 3.22: 15492 3.22 - 3.78: 26605 3.78 - 4.34: 31000 4.34 - 4.90: 50887 Nonbonded interactions: 124145 Sorted by model distance: nonbonded pdb=" OE1 GLU B 144 " pdb=" NH2 ARG B 147 " model vdw 2.095 3.120 nonbonded pdb=" OE1 GLU A 144 " pdb=" NH2 ARG A 147 " model vdw 2.095 3.120 nonbonded pdb=" OE1 GLU C 144 " pdb=" NH2 ARG C 147 " model vdw 2.095 3.120 nonbonded pdb=" OE1 GLU D 144 " pdb=" NH2 ARG D 147 " model vdw 2.095 3.120 nonbonded pdb=" OE2 GLU C 144 " pdb=" NH2 ARG C 147 " model vdw 2.106 3.120 ... (remaining 124140 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.020 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.290 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15600 Z= 0.319 Angle : 0.871 10.932 20904 Z= 0.467 Chirality : 0.044 0.375 2588 Planarity : 0.003 0.023 2668 Dihedral : 14.516 87.915 6160 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 1976 helix: 1.15 (0.10), residues: 1892 sheet: None (None), residues: 0 loop : -3.42 (0.40), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 383 PHE 0.009 0.002 PHE A 106 TYR 0.001 0.001 TYR D 416 ARG 0.003 0.000 ARG D 330 Details of bonding type rmsd hydrogen bonds : bond 0.06981 ( 1677) hydrogen bonds : angle 4.05209 ( 5031) covalent geometry : bond 0.00730 (15600) covalent geometry : angle 0.87096 (20904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.682 Fit side-chains REVERT: A 195 MET cc_start: 0.8114 (tpt) cc_final: 0.7733 (tpt) REVERT: B 10 GLU cc_start: 0.8331 (tp30) cc_final: 0.8055 (tp30) REVERT: B 195 MET cc_start: 0.8077 (tpt) cc_final: 0.7751 (tpt) REVERT: C 195 MET cc_start: 0.8076 (tpt) cc_final: 0.7772 (tpt) REVERT: D 10 GLU cc_start: 0.8326 (tp30) cc_final: 0.8085 (tp30) REVERT: D 195 MET cc_start: 0.8156 (tpt) cc_final: 0.7784 (tpt) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2590 time to fit residues: 101.1107 Evaluate side-chains 141 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 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 = 0.4560 r_free = 0.4560 target = 0.165037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.142944 restraints weight = 13924.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.146609 restraints weight = 7833.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.149149 restraints weight = 5548.910| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15600 Z= 0.123 Angle : 0.528 9.246 20904 Z= 0.258 Chirality : 0.030 0.133 2588 Planarity : 0.002 0.019 2668 Dihedral : 3.773 23.392 2112 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 10.32 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.17), residues: 1976 helix: 2.84 (0.11), residues: 1892 sheet: None (None), residues: 0 loop : -2.67 (0.53), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 383 PHE 0.007 0.001 PHE B 106 TYR 0.002 0.000 TYR A 416 ARG 0.003 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 1677) hydrogen bonds : angle 3.15745 ( 5031) covalent geometry : bond 0.00281 (15600) covalent geometry : angle 0.52765 (20904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.841 Fit side-chains REVERT: A 10 GLU cc_start: 0.8271 (tp30) cc_final: 0.8004 (tp30) REVERT: A 81 ARG cc_start: 0.7392 (tpt170) cc_final: 0.7074 (tpp-160) REVERT: A 227 GLU cc_start: 0.6624 (tm-30) cc_final: 0.6245 (tm-30) REVERT: B 18 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8046 (mt) REVERT: B 81 ARG cc_start: 0.7432 (tpt170) cc_final: 0.7105 (tpp-160) REVERT: C 18 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8029 (mt) REVERT: C 81 ARG cc_start: 0.7439 (tpt170) cc_final: 0.7087 (tpp-160) REVERT: C 216 GLU cc_start: 0.6998 (tp30) cc_final: 0.6422 (tm-30) REVERT: C 227 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6297 (tm-30) REVERT: D 81 ARG cc_start: 0.7433 (tpt170) cc_final: 0.7120 (tpp-160) outliers start: 23 outliers final: 21 residues processed: 182 average time/residue: 0.2781 time to fit residues: 75.8474 Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 483 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 118 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 118 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 118 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.160929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.139016 restraints weight = 13947.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.142788 restraints weight = 7696.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.145300 restraints weight = 5409.658| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15600 Z= 0.150 Angle : 0.558 8.753 20904 Z= 0.268 Chirality : 0.031 0.138 2588 Planarity : 0.002 0.012 2668 Dihedral : 3.696 22.889 2112 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.86 % Allowed : 12.75 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.17), residues: 1976 helix: 3.14 (0.10), residues: 1904 sheet: None (None), residues: 0 loop : -3.45 (0.43), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 383 PHE 0.007 0.001 PHE B 106 TYR 0.001 0.000 TYR D 416 ARG 0.002 0.000 ARG C 311 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1677) hydrogen bonds : angle 3.15105 ( 5031) covalent geometry : bond 0.00353 (15600) covalent geometry : angle 0.55778 (20904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.722 Fit side-chains REVERT: A 47 GLU cc_start: 0.5378 (mm-30) cc_final: 0.4611 (tm-30) REVERT: B 47 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4776 (tm-30) REVERT: C 47 GLU cc_start: 0.5558 (mm-30) cc_final: 0.4742 (tm-30) REVERT: D 47 GLU cc_start: 0.5566 (mm-30) cc_final: 0.4784 (tm-30) outliers start: 46 outliers final: 37 residues processed: 184 average time/residue: 0.2676 time to fit residues: 74.4689 Evaluate side-chains 178 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 448 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 = 0.4542 r_free = 0.4542 target = 0.163189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.140468 restraints weight = 14184.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.144124 restraints weight = 8196.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.146631 restraints weight = 5888.238| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15600 Z= 0.154 Angle : 0.559 14.345 20904 Z= 0.269 Chirality : 0.031 0.136 2588 Planarity : 0.002 0.015 2668 Dihedral : 3.669 22.978 2112 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.11 % Allowed : 15.36 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.17), residues: 1976 helix: 3.33 (0.10), residues: 1908 sheet: None (None), residues: 0 loop : -3.58 (0.47), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 383 PHE 0.008 0.001 PHE B 401 TYR 0.001 0.000 TYR C 416 ARG 0.002 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1677) hydrogen bonds : angle 3.11470 ( 5031) covalent geometry : bond 0.00369 (15600) covalent geometry : angle 0.55893 (20904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 1.711 Fit side-chains REVERT: A 47 GLU cc_start: 0.5614 (mm-30) cc_final: 0.4613 (tm-30) REVERT: B 47 GLU cc_start: 0.5702 (mm-30) cc_final: 0.4710 (tm-30) REVERT: B 482 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 47 GLU cc_start: 0.5664 (mm-30) cc_final: 0.4683 (tm-30) REVERT: D 47 GLU cc_start: 0.5746 (mm-30) cc_final: 0.4739 (tm-30) REVERT: D 227 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6274 (tm-30) outliers start: 50 outliers final: 40 residues processed: 193 average time/residue: 0.2565 time to fit residues: 75.4029 Evaluate side-chains 178 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 448 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 = 0.4891 r_free = 0.4891 target = 0.263425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.4922 r_free = 0.4922 target = 0.228312 restraints weight = 17121.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.228102 restraints weight = 19721.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.228027 restraints weight = 19838.162| |-----------------------------------------------------------------------------| r_work (final): 0.4834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15600 Z= 0.130 Angle : 0.543 13.225 20904 Z= 0.262 Chirality : 0.029 0.122 2588 Planarity : 0.002 0.009 2668 Dihedral : 3.590 23.146 2112 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.36 % Allowed : 16.23 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.15 (0.17), residues: 1976 helix: 3.54 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.76 (0.51), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 383 PHE 0.008 0.001 PHE B 106 TYR 0.001 0.000 TYR B 416 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 1677) hydrogen bonds : angle 3.02684 ( 5031) covalent geometry : bond 0.00310 (15600) covalent geometry : angle 0.54273 (20904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 1.720 Fit side-chains REVERT: A 227 GLU cc_start: 0.6420 (tm-30) cc_final: 0.6057 (tm-30) REVERT: D 227 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6185 (tm-30) outliers start: 54 outliers final: 46 residues processed: 184 average time/residue: 0.2408 time to fit residues: 68.9549 Evaluate side-chains 186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.155159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.132453 restraints weight = 14465.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.136078 restraints weight = 8229.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.138217 restraints weight = 5882.730| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15600 Z= 0.236 Angle : 0.695 9.408 20904 Z= 0.334 Chirality : 0.034 0.144 2588 Planarity : 0.003 0.028 2668 Dihedral : 3.858 22.863 2112 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.79 % Allowed : 16.48 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.17), residues: 1976 helix: 3.02 (0.10), residues: 1908 sheet: None (None), residues: 0 loop : -3.46 (0.58), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 383 PHE 0.011 0.002 PHE B 401 TYR 0.001 0.000 TYR C 416 ARG 0.002 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1677) hydrogen bonds : angle 3.36048 ( 5031) covalent geometry : bond 0.00566 (15600) covalent geometry : angle 0.69505 (20904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 1.734 Fit side-chains REVERT: A 33 LEU cc_start: 0.8302 (mt) cc_final: 0.7938 (tt) REVERT: B 33 LEU cc_start: 0.8325 (mt) cc_final: 0.7973 (tt) REVERT: B 35 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6962 (mm-30) outliers start: 77 outliers final: 61 residues processed: 213 average time/residue: 0.2409 time to fit residues: 80.5323 Evaluate side-chains 198 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 483 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.264024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 161)---------------| | r_work = 0.4902 r_free = 0.4902 target = 0.229313 restraints weight = 17185.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.229038 restraints weight = 21579.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.228897 restraints weight = 20883.087| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15600 Z= 0.130 Angle : 0.546 10.232 20904 Z= 0.271 Chirality : 0.029 0.115 2588 Planarity : 0.002 0.017 2668 Dihedral : 3.608 23.641 2112 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.61 % Allowed : 18.66 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.16 (0.17), residues: 1976 helix: 3.53 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.59 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 265 PHE 0.008 0.001 PHE B 401 TYR 0.002 0.000 TYR C 416 ARG 0.002 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1677) hydrogen bonds : angle 3.06460 ( 5031) covalent geometry : bond 0.00313 (15600) covalent geometry : angle 0.54626 (20904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.704 Fit side-chains REVERT: A 227 GLU cc_start: 0.6347 (tm-30) cc_final: 0.6078 (tm-30) REVERT: A 317 MET cc_start: 0.7356 (ttm) cc_final: 0.7149 (ttp) REVERT: B 172 GLU cc_start: 0.5802 (tm-30) cc_final: 0.5460 (tm-30) REVERT: B 280 GLU cc_start: 0.7765 (tp30) cc_final: 0.7544 (mm-30) REVERT: C 280 GLU cc_start: 0.7746 (tp30) cc_final: 0.7538 (mm-30) REVERT: D 172 GLU cc_start: 0.5848 (tm-30) cc_final: 0.5499 (tm-30) REVERT: D 280 GLU cc_start: 0.7737 (tp30) cc_final: 0.7531 (mm-30) outliers start: 58 outliers final: 50 residues processed: 211 average time/residue: 0.2472 time to fit residues: 80.5231 Evaluate side-chains 202 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 46 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 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 = 0.4893 r_free = 0.4893 target = 0.262103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4889 r_free = 0.4889 target = 0.230833 restraints weight = 17120.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.228736 restraints weight = 16788.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.228350 restraints weight = 18134.310| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15600 Z= 0.147 Angle : 0.574 11.155 20904 Z= 0.278 Chirality : 0.030 0.124 2588 Planarity : 0.002 0.021 2668 Dihedral : 3.625 23.292 2112 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.04 % Allowed : 18.91 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.16 (0.17), residues: 1976 helix: 3.54 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.66 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 383 PHE 0.009 0.002 PHE A 401 TYR 0.001 0.000 TYR B 416 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 1677) hydrogen bonds : angle 3.08858 ( 5031) covalent geometry : bond 0.00355 (15600) covalent geometry : angle 0.57361 (20904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.772 Fit side-chains REVERT: A 227 GLU cc_start: 0.6409 (tm-30) cc_final: 0.6106 (tm-30) REVERT: A 317 MET cc_start: 0.7376 (ttm) cc_final: 0.7161 (ttp) REVERT: B 227 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6248 (tm-30) REVERT: B 280 GLU cc_start: 0.7748 (tp30) cc_final: 0.7546 (mm-30) REVERT: D 227 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6272 (tm-30) outliers start: 65 outliers final: 51 residues processed: 215 average time/residue: 0.2292 time to fit residues: 78.1305 Evaluate side-chains 200 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 167 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN D 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.260194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 197)---------------| | r_work = 0.4840 r_free = 0.4840 target = 0.224720 restraints weight = 17203.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.224048 restraints weight = 22644.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.224048 restraints weight = 23636.629| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15600 Z= 0.179 Angle : 0.628 9.705 20904 Z= 0.301 Chirality : 0.031 0.136 2588 Planarity : 0.003 0.034 2668 Dihedral : 3.711 23.372 2112 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.98 % Allowed : 19.28 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.17), residues: 1976 helix: 3.36 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.74 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 383 PHE 0.010 0.002 PHE C 401 TYR 0.000 0.000 TYR B 416 ARG 0.004 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 1677) hydrogen bonds : angle 3.18924 ( 5031) covalent geometry : bond 0.00437 (15600) covalent geometry : angle 0.62844 (20904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 1.770 Fit side-chains REVERT: A 317 MET cc_start: 0.7304 (ttm) cc_final: 0.7094 (ttp) REVERT: C 484 MET cc_start: 0.7781 (ttp) cc_final: 0.7575 (ttp) REVERT: D 227 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6224 (tm-30) outliers start: 64 outliers final: 57 residues processed: 213 average time/residue: 0.2452 time to fit residues: 82.1620 Evaluate side-chains 208 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 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 = 0.4909 r_free = 0.4909 target = 0.263910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 218)---------------| | r_work = 0.4903 r_free = 0.4903 target = 0.228915 restraints weight = 17180.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.228694 restraints weight = 21346.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.228613 restraints weight = 21792.203| |-----------------------------------------------------------------------------| r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15600 Z= 0.132 Angle : 0.568 10.531 20904 Z= 0.277 Chirality : 0.029 0.130 2588 Planarity : 0.002 0.022 2668 Dihedral : 3.585 23.390 2112 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.67 % Allowed : 19.65 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.35 (0.17), residues: 1976 helix: 3.66 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.67 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 383 PHE 0.012 0.001 PHE D 401 TYR 0.001 0.000 TYR C 416 ARG 0.004 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 1677) hydrogen bonds : angle 3.03808 ( 5031) covalent geometry : bond 0.00320 (15600) covalent geometry : angle 0.56771 (20904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 1.763 Fit side-chains REVERT: A 227 GLU cc_start: 0.6339 (tm-30) cc_final: 0.6006 (tm-30) REVERT: A 280 GLU cc_start: 0.7753 (tp30) cc_final: 0.7429 (mm-30) REVERT: B 227 GLU cc_start: 0.6370 (tm-30) cc_final: 0.6104 (tm-30) REVERT: D 227 GLU cc_start: 0.6402 (tm-30) cc_final: 0.6115 (tm-30) outliers start: 59 outliers final: 52 residues processed: 218 average time/residue: 0.2406 time to fit residues: 83.2487 Evaluate side-chains 210 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 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 = 0.4912 r_free = 0.4912 target = 0.262921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.4906 r_free = 0.4906 target = 0.228343 restraints weight = 17114.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.227421 restraints weight = 20460.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.227358 restraints weight = 23938.537| |-----------------------------------------------------------------------------| r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15600 Z= 0.136 Angle : 0.583 15.954 20904 Z= 0.280 Chirality : 0.029 0.125 2588 Planarity : 0.002 0.047 2668 Dihedral : 3.566 23.086 2112 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.79 % Allowed : 19.84 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.43 (0.17), residues: 1976 helix: 3.71 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.72 (0.60), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 383 PHE 0.017 0.001 PHE C 401 TYR 0.001 0.000 TYR C 416 ARG 0.008 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 1677) hydrogen bonds : angle 3.01877 ( 5031) covalent geometry : bond 0.00332 (15600) covalent geometry : angle 0.58309 (20904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.65 seconds wall clock time: 73 minutes 51.58 seconds (4431.58 seconds total)