Starting phenix.real_space_refine on Mon Nov 18 02:04:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_29974.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_29974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_29974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_29974.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gel_29974/11_2024/8gel_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-5513/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: 8.21, per 1000 atoms: 0.53 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 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: 0.92 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: 5.44 Time building geometry restraints manager: 4.72 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 34.520 Find NCS groups from input model: 0.470 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- 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= 0.466 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 *********************** 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 : 1.777 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: 0.2729 time to fit residues: 106.4871 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 : 1.786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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= 0.178 Angle : 0.528 9.246 20904 Z= 0.258 Chirality : 0.030 0.133 2588 Planarity : 0.002 0.018 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 *********************** 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 : 1.752 Fit side-chains REVERT: A 10 GLU cc_start: 0.8109 (tp30) cc_final: 0.7872 (tp30) REVERT: A 81 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7167 (tpp-160) REVERT: A 227 GLU cc_start: 0.6426 (tm-30) cc_final: 0.6082 (tm-30) REVERT: B 18 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8088 (mt) REVERT: B 81 ARG cc_start: 0.7447 (tpt170) cc_final: 0.7187 (tpp-160) REVERT: C 18 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 81 ARG cc_start: 0.7461 (tpt170) cc_final: 0.7178 (tpp-160) REVERT: C 216 GLU cc_start: 0.6706 (tp30) cc_final: 0.6364 (tm-30) REVERT: C 227 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6132 (tm-30) REVERT: D 81 ARG cc_start: 0.7445 (tpt170) cc_final: 0.7216 (tpp-160) outliers start: 23 outliers final: 21 residues processed: 182 average time/residue: 0.2984 time to fit residues: 81.7424 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 : 1.791 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15600 Z= 0.212 Angle : 0.543 8.349 20904 Z= 0.262 Chirality : 0.030 0.136 2588 Planarity : 0.002 0.012 2668 Dihedral : 3.679 22.794 2112 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 12.75 % Favored : 84.45 % 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: 4.59 (0.17), residues: 1976 helix: 3.19 (0.10), residues: 1904 sheet: None (None), residues: 0 loop : -3.47 (0.43), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 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 *********************** 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 198 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.628 Fit side-chains REVERT: A 47 GLU cc_start: 0.5521 (mm-30) cc_final: 0.4843 (tm-30) REVERT: B 47 GLU cc_start: 0.5740 (mm-30) cc_final: 0.5046 (tm-30) REVERT: C 47 GLU cc_start: 0.5758 (mm-30) cc_final: 0.5057 (tm-30) REVERT: D 47 GLU cc_start: 0.5768 (mm-30) cc_final: 0.5072 (tm-30) outliers start: 45 outliers final: 36 residues processed: 185 average time/residue: 0.2807 time to fit residues: 77.8062 Evaluate side-chains 179 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 176 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2390 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= 0.186 Angle : 0.507 12.191 20904 Z= 0.249 Chirality : 0.029 0.133 2588 Planarity : 0.002 0.012 2668 Dihedral : 3.578 22.951 2112 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.11 % Allowed : 14.61 % Favored : 82.28 % 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: 5.10 (0.17), residues: 1976 helix: 3.50 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.84 (0.44), 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 C 416 ARG 0.002 0.000 ARG A 463 *********************** 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 200 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 1.759 Fit side-chains REVERT: A 47 GLU cc_start: 0.5577 (mm-30) cc_final: 0.4747 (tm-30) REVERT: B 47 GLU cc_start: 0.5695 (mm-30) cc_final: 0.4836 (tm-30) REVERT: C 47 GLU cc_start: 0.5637 (mm-30) cc_final: 0.4828 (tm-30) REVERT: D 47 GLU cc_start: 0.5679 (mm-30) cc_final: 0.4828 (tm-30) REVERT: D 227 GLU cc_start: 0.6361 (tm-30) cc_final: 0.6120 (tm-30) outliers start: 50 outliers final: 37 residues processed: 191 average time/residue: 0.2765 time to fit residues: 79.9588 Evaluate side-chains 179 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 212 LEU 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 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 347 ILE 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 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 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 157 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2574 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= 0.195 Angle : 0.513 12.920 20904 Z= 0.250 Chirality : 0.029 0.127 2588 Planarity : 0.002 0.008 2668 Dihedral : 3.548 22.937 2112 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.99 % Allowed : 15.61 % Favored : 81.41 % 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: 5.25 (0.17), residues: 1976 helix: 3.60 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.84 (0.46), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 383 PHE 0.008 0.001 PHE B 106 TYR 0.001 0.000 TYR B 416 ARG 0.002 0.000 ARG A 463 *********************** 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 192 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.800 Fit side-chains REVERT: A 47 GLU cc_start: 0.5712 (mm-30) cc_final: 0.4755 (tm-30) REVERT: A 227 GLU cc_start: 0.6415 (tm-30) cc_final: 0.6150 (tm-30) REVERT: B 47 GLU cc_start: 0.5767 (mm-30) cc_final: 0.4863 (tm-30) REVERT: C 47 GLU cc_start: 0.5710 (mm-30) cc_final: 0.4833 (tm-30) REVERT: D 47 GLU cc_start: 0.5764 (mm-30) cc_final: 0.4856 (tm-30) REVERT: D 227 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6067 (tm-30) outliers start: 48 outliers final: 40 residues processed: 176 average time/residue: 0.2577 time to fit residues: 70.4289 Evaluate side-chains 175 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 212 LEU 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 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 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 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 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 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 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15600 Z= 0.168 Angle : 0.493 15.609 20904 Z= 0.244 Chirality : 0.028 0.115 2588 Planarity : 0.002 0.011 2668 Dihedral : 3.473 22.575 2112 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.36 % Allowed : 16.92 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.54 (0.17), residues: 1976 helix: 3.78 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.90 (0.44), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 383 PHE 0.009 0.001 PHE C 401 TYR 0.001 0.000 TYR B 416 ARG 0.002 0.000 ARG B 463 *********************** 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 194 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.817 Fit side-chains REVERT: A 227 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6106 (tm-30) REVERT: D 47 GLU cc_start: 0.5770 (mm-30) cc_final: 0.4846 (tm-30) REVERT: D 227 GLU cc_start: 0.6295 (tm-30) cc_final: 0.6084 (tm-30) outliers start: 38 outliers final: 33 residues processed: 188 average time/residue: 0.2538 time to fit residues: 73.8241 Evaluate side-chains 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 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 257 VAL 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 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 347 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 18 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 347 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 142 SER 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 347 ILE Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15600 Z= 0.167 Angle : 0.505 9.728 20904 Z= 0.244 Chirality : 0.028 0.113 2588 Planarity : 0.002 0.013 2668 Dihedral : 3.440 22.330 2112 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.74 % Allowed : 17.97 % Favored : 79.29 % 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: 5.67 (0.17), residues: 1976 helix: 3.86 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -3.92 (0.45), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 383 PHE 0.007 0.001 PHE A 106 TYR 0.001 0.000 TYR C 416 ARG 0.002 0.000 ARG A 81 *********************** 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 207 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 1.712 Fit side-chains REVERT: B 195 MET cc_start: 0.7928 (tpt) cc_final: 0.7710 (tpp) REVERT: B 202 ASN cc_start: 0.8033 (t0) cc_final: 0.7706 (t0) REVERT: B 227 GLU cc_start: 0.6252 (tm-30) cc_final: 0.5916 (tm-30) REVERT: B 484 MET cc_start: 0.7149 (ttm) cc_final: 0.6889 (ttm) REVERT: C 195 MET cc_start: 0.7913 (tpt) cc_final: 0.7695 (tpp) REVERT: C 202 ASN cc_start: 0.8049 (t0) cc_final: 0.7740 (t0) REVERT: C 227 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5920 (tm-30) REVERT: C 280 GLU cc_start: 0.7624 (tp30) cc_final: 0.7408 (mm-30) REVERT: D 195 MET cc_start: 0.7860 (tpt) cc_final: 0.7637 (tpp) REVERT: D 202 ASN cc_start: 0.8031 (t0) cc_final: 0.7733 (t0) REVERT: D 227 GLU cc_start: 0.6289 (tm-30) cc_final: 0.6042 (tm-30) REVERT: D 484 MET cc_start: 0.7399 (ttp) cc_final: 0.7109 (ttm) outliers start: 44 outliers final: 41 residues processed: 202 average time/residue: 0.2482 time to fit residues: 79.1316 Evaluate side-chains 193 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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 347 ILE Chi-restraints excluded: chain A residue 357 LEU 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 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 347 ILE 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 235 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 448 ASN 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 235 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 347 ILE 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 116 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15600 Z= 0.167 Angle : 0.486 7.279 20904 Z= 0.240 Chirality : 0.028 0.112 2588 Planarity : 0.002 0.012 2668 Dihedral : 3.409 22.096 2112 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.61 % Allowed : 17.04 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.73 (0.17), residues: 1976 helix: 3.90 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -3.98 (0.44), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 383 PHE 0.007 0.001 PHE B 106 TYR 0.001 0.000 TYR C 416 ARG 0.002 0.000 ARG B 81 *********************** 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 212 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 1.776 Fit side-chains REVERT: B 198 MET cc_start: 0.6283 (ttm) cc_final: 0.6064 (ttm) REVERT: B 227 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5875 (tm-30) REVERT: B 484 MET cc_start: 0.7089 (ttm) cc_final: 0.6875 (ttm) REVERT: C 227 GLU cc_start: 0.6333 (tm-30) cc_final: 0.5923 (tm-30) REVERT: C 280 GLU cc_start: 0.7616 (tp30) cc_final: 0.7381 (tm-30) outliers start: 58 outliers final: 45 residues processed: 204 average time/residue: 0.2528 time to fit residues: 80.5422 Evaluate side-chains 194 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU 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 347 ILE 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 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 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 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 347 ILE 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 171 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15600 Z= 0.260 Angle : 0.590 9.866 20904 Z= 0.284 Chirality : 0.031 0.146 2588 Planarity : 0.002 0.027 2668 Dihedral : 3.563 22.414 2112 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.73 % Allowed : 17.10 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.24 (0.17), residues: 1976 helix: 3.60 (0.10), residues: 1912 sheet: None (None), residues: 0 loop : -3.98 (0.48), 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 106 TYR 0.001 0.000 TYR A 416 ARG 0.004 0.000 ARG A 81 *********************** 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 217 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 1.810 Fit side-chains REVERT: B 227 GLU cc_start: 0.6369 (tm-30) cc_final: 0.6066 (tm-30) REVERT: C 227 GLU cc_start: 0.6338 (tm-30) cc_final: 0.6047 (tm-30) REVERT: D 81 ARG cc_start: 0.7422 (tpp-160) cc_final: 0.7201 (tpp-160) outliers start: 60 outliers final: 47 residues processed: 211 average time/residue: 0.2449 time to fit residues: 80.6555 Evaluate side-chains 202 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 292 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 488 LEU Chi-restraints excluded: chain B residue 7 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 347 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 488 LEU 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 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 C residue 488 LEU Chi-restraints excluded: chain D residue 7 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 347 ILE Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15600 Z= 0.189 Angle : 0.551 14.874 20904 Z= 0.269 Chirality : 0.028 0.126 2588 Planarity : 0.002 0.021 2668 Dihedral : 3.477 22.866 2112 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.74 % Allowed : 18.16 % Favored : 79.10 % 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: 5.61 (0.17), residues: 1976 helix: 3.82 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -3.88 (0.53), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 265 PHE 0.009 0.001 PHE C 401 TYR 0.001 0.000 TYR B 416 ARG 0.002 0.000 ARG A 81 ********************** 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 209 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.800 Fit side-chains REVERT: B 172 GLU cc_start: 0.5640 (tm-30) cc_final: 0.5388 (tm-30) REVERT: C 172 GLU cc_start: 0.5629 (tm-30) cc_final: 0.5364 (tm-30) REVERT: D 172 GLU cc_start: 0.5616 (tm-30) cc_final: 0.5363 (tm-30) REVERT: D 280 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7303 (mm-30) outliers start: 44 outliers final: 42 residues processed: 209 average time/residue: 0.2695 time to fit residues: 85.8053 Evaluate side-chains 192 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 ILE 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 347 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 7 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 347 ILE Chi-restraints excluded: chain B residue 488 LEU 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 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 405 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 69 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 = 0.4919 r_free = 0.4919 target = 0.264183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 178)---------------| | r_work = 0.4934 r_free = 0.4934 target = 0.229256 restraints weight = 16962.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.228959 restraints weight = 23424.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.228933 restraints weight = 22720.226| |-----------------------------------------------------------------------------| r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3324 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= 0.199 Angle : 0.568 18.433 20904 Z= 0.272 Chirality : 0.029 0.135 2588 Planarity : 0.002 0.024 2668 Dihedral : 3.460 22.670 2112 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.05 % Allowed : 18.16 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.62 (0.17), residues: 1976 helix: 3.83 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -3.93 (0.52), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 383 PHE 0.008 0.001 PHE C 106 TYR 0.001 0.000 TYR D 416 ARG 0.006 0.000 ARG B 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.53 seconds wall clock time: 47 minutes 31.63 seconds (2851.63 seconds total)