Starting phenix.real_space_refine on Mon Apr 28 02:38:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.map" model { file = "/net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mty_48616/04_2025/9mty_48616.cif" } resolution = 3.05 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: 6 Type Number sf(0) Gaussians P 111 5.49 5 Mg 4 5.21 5 S 8 5.16 5 C 4140 2.51 5 N 1279 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7106 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2384 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2401 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 2 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 759 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 10, 'rna3p': 25} Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.64, per 1000 atoms: 0.65 Number of scatterers: 7106 At special positions: 0 Unit cell: (82.7274, 94.5456, 86.6668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 111 15.00 Mg 4 11.99 O 1564 8.00 N 1279 7.00 C 4140 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: 1.93 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 64.8% alpha, 5.3% beta 41 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.947A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 removed outlier: 4.163A pdb=" N SER A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 165 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.742A pdb=" N PHE A 199 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 230 through 248 removed outlier: 4.090A pdb=" N ARG A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.718A pdb=" N GLU A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.662A pdb=" N ALA A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 66 through 72 Processing helix chain 'B' and resid 73 through 74 No H-bonds generated for 'chain 'B' and resid 73 through 74' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 112 through 138 removed outlier: 3.980A pdb=" N SER B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 165 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.885A pdb=" N ARG B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.506A pdb=" N GLU B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 269 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AA3, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.621A pdb=" N ALA B 20 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 40 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 213 through 214 280 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1086 1.32 - 1.44: 2512 1.44 - 1.56: 3660 1.56 - 1.68: 218 1.68 - 1.80: 12 Bond restraints: 7488 Sorted by residual: bond pdb=" CB ILE B 233 " pdb=" CG2 ILE B 233 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" O5' C C 27 " pdb=" C5' C C 27 " ideal model delta sigma weight residual 1.420 1.389 0.031 1.50e-02 4.44e+03 4.20e+00 bond pdb=" CB ARG A 130 " pdb=" CG ARG A 130 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.14e+00 bond pdb=" CB ASN B 239 " pdb=" CG ASN B 239 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" N9 G C 32 " pdb=" C4 G C 32 " ideal model delta sigma weight residual 1.375 1.336 0.039 2.00e-02 2.50e+03 3.85e+00 ... (remaining 7483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9804 2.14 - 4.28: 718 4.28 - 6.42: 73 6.42 - 8.56: 6 8.56 - 10.71: 2 Bond angle restraints: 10603 Sorted by residual: angle pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " pdb=" N9 DG D -5 " ideal model delta sigma weight residual 108.40 117.56 -9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C4' DG D -5 " pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " ideal model delta sigma weight residual 109.70 102.68 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C2' G C 2 " pdb=" C1' G C 2 " pdb=" N9 G C 2 " ideal model delta sigma weight residual 112.00 118.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" C3' A C 18 " pdb=" O3' A C 18 " pdb=" P A C 19 " ideal model delta sigma weight residual 120.20 127.07 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" O4' DA D -6 " pdb=" C1' DA D -6 " pdb=" N9 DA D -6 " ideal model delta sigma weight residual 108.40 115.23 -6.83 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 3868 30.32 - 60.64: 426 60.64 - 90.95: 48 90.95 - 121.27: 2 121.27 - 151.59: 2 Dihedral angle restraints: 4346 sinusoidal: 2624 harmonic: 1722 Sorted by residual: dihedral pdb=" C3' A C 19 " pdb=" C4' A C 19 " pdb=" O4' A C 19 " pdb=" C1' A C 19 " ideal model delta sinusoidal sigma weight residual 20.00 -24.76 44.76 1 8.00e+00 1.56e-02 4.35e+01 dihedral pdb=" O4' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" C2' A C 19 " ideal model delta sinusoidal sigma weight residual -35.00 9.40 -44.40 1 8.00e+00 1.56e-02 4.28e+01 dihedral pdb=" C5' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" O3' A C 19 " ideal model delta sinusoidal sigma weight residual 82.00 124.70 -42.70 1 8.00e+00 1.56e-02 3.98e+01 ... (remaining 4343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 837 0.076 - 0.153: 298 0.153 - 0.229: 33 0.229 - 0.306: 11 0.306 - 0.382: 5 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1' DG D -5 " pdb=" O4' DG D -5 " pdb=" C2' DG D -5 " pdb=" N9 DG D -5 " both_signs ideal model delta sigma weight residual False 2.42 2.04 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' DC F 4 " pdb=" O4' DC F 4 " pdb=" C2' DC F 4 " pdb=" N1 DC F 4 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1181 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 20 " 0.088 2.00e-02 2.50e+03 5.43e-02 6.65e+01 pdb=" N1 C C 20 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C C 20 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C C 20 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C C 20 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C C 20 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C C 20 " 0.067 2.00e-02 2.50e+03 pdb=" C6 C C 20 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D -6 " 0.045 2.00e-02 2.50e+03 2.89e-02 2.30e+01 pdb=" N9 DA D -6 " -0.082 2.00e-02 2.50e+03 pdb=" C8 DA D -6 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA D -6 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA D -6 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA D -6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D -6 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA D -6 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 32 " 0.044 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G C 32 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 32 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G C 32 " -0.019 2.00e-02 2.50e+03 pdb=" C5 G C 32 " -0.028 2.00e-02 2.50e+03 pdb=" C6 G C 32 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G C 32 " 0.061 2.00e-02 2.50e+03 pdb=" N1 G C 32 " -0.023 2.00e-02 2.50e+03 pdb=" C2 G C 32 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 32 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G C 32 " 0.017 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 37 2.62 - 3.19: 5891 3.19 - 3.76: 12147 3.76 - 4.33: 17191 4.33 - 4.90: 25349 Nonbonded interactions: 60615 Sorted by model distance: nonbonded pdb=" OD1 ASP B 11 " pdb="MG MG B 401 " model vdw 2.052 2.170 nonbonded pdb=" OD1 ASP B 123 " pdb="MG MG B 402 " model vdw 2.171 2.170 nonbonded pdb=" OP1 U C 29 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG MG A 401 " model vdw 2.235 2.170 nonbonded pdb=" OD1 ASP A 123 " pdb="MG MG A 402 " model vdw 2.254 2.170 ... (remaining 60610 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' and (resid 6 through 303 or resid 318 through 322 or resid 401 throug \ h 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 7488 Z= 0.420 Angle : 1.159 10.705 10603 Z= 0.699 Chirality : 0.078 0.382 1184 Planarity : 0.014 0.137 952 Dihedral : 21.340 151.590 3230 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.39 % Allowed : 4.69 % Favored : 94.92 % 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: -0.43 (0.32), residues: 574 helix: -0.79 (0.22), residues: 333 sheet: -0.08 (0.74), residues: 46 loop : 1.09 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 321 HIS 0.015 0.004 HIS B 320 PHE 0.030 0.005 PHE A 22 TYR 0.040 0.008 TYR B 208 ARG 0.027 0.003 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.11966 ( 382) hydrogen bonds : angle 5.22893 ( 1017) covalent geometry : bond 0.00908 ( 7488) covalent geometry : angle 1.15908 (10603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.637 Fit side-chains REVERT: A 145 GLU cc_start: 0.6966 (tp30) cc_final: 0.6679 (mm-30) REVERT: A 152 LYS cc_start: 0.7882 (tttt) cc_final: 0.7526 (mtmt) REVERT: B 149 ILE cc_start: 0.8130 (mt) cc_final: 0.7740 (mm) REVERT: B 163 LYS cc_start: 0.7615 (tttt) cc_final: 0.7271 (ttmm) REVERT: B 202 VAL cc_start: 0.8466 (t) cc_final: 0.8262 (m) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.2480 time to fit residues: 41.0069 Evaluate side-chains 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 272 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.186712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150208 restraints weight = 7140.702| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.20 r_work: 0.3372 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7488 Z= 0.185 Angle : 0.696 9.698 10603 Z= 0.397 Chirality : 0.045 0.252 1184 Planarity : 0.006 0.050 952 Dihedral : 24.863 150.487 2028 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.39 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 7.03 % Favored : 91.02 % 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: 1.73 (0.34), residues: 574 helix: 1.27 (0.27), residues: 335 sheet: 0.09 (0.72), residues: 47 loop : 1.56 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 95 HIS 0.006 0.001 HIS A 168 PHE 0.024 0.002 PHE B 22 TYR 0.020 0.002 TYR A 289 ARG 0.005 0.001 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 382) hydrogen bonds : angle 3.84591 ( 1017) covalent geometry : bond 0.00398 ( 7488) covalent geometry : angle 0.69580 (10603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.649 Fit side-chains REVERT: A 152 LYS cc_start: 0.8107 (tttt) cc_final: 0.7668 (mtpt) REVERT: A 162 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: A 172 THR cc_start: 0.7187 (p) cc_final: 0.6969 (t) REVERT: B 149 ILE cc_start: 0.8207 (mt) cc_final: 0.7794 (mm) REVERT: B 163 LYS cc_start: 0.7830 (tttt) cc_final: 0.7414 (ttmm) outliers start: 10 outliers final: 3 residues processed: 105 average time/residue: 0.2661 time to fit residues: 34.7389 Evaluate side-chains 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.190323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155463 restraints weight = 7430.176| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.19 r_work: 0.3425 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7488 Z= 0.148 Angle : 0.595 9.910 10603 Z= 0.339 Chirality : 0.041 0.209 1184 Planarity : 0.005 0.040 952 Dihedral : 25.003 154.823 2028 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.37 % Allowed : 9.18 % Favored : 89.45 % 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: 2.64 (0.36), residues: 574 helix: 2.10 (0.28), residues: 336 sheet: 0.09 (0.71), residues: 47 loop : 1.82 (0.51), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.004 0.001 HIS A 168 PHE 0.014 0.002 PHE B 22 TYR 0.009 0.001 TYR B 117 ARG 0.004 0.000 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 382) hydrogen bonds : angle 3.53221 ( 1017) covalent geometry : bond 0.00314 ( 7488) covalent geometry : angle 0.59527 (10603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.723 Fit side-chains REVERT: A 40 ILE cc_start: 0.6958 (mp) cc_final: 0.6729 (mp) REVERT: A 140 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7284 (p) REVERT: A 162 ASP cc_start: 0.6919 (t0) cc_final: 0.6624 (m-30) REVERT: B 149 ILE cc_start: 0.8241 (mt) cc_final: 0.7813 (mm) REVERT: B 163 LYS cc_start: 0.7728 (tttt) cc_final: 0.7070 (mttm) REVERT: B 173 GLN cc_start: 0.7574 (mt0) cc_final: 0.7251 (mm110) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.3170 time to fit residues: 41.1329 Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 287 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.189960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153761 restraints weight = 7416.204| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.29 r_work: 0.3394 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7488 Z= 0.141 Angle : 0.573 9.803 10603 Z= 0.328 Chirality : 0.040 0.213 1184 Planarity : 0.004 0.053 952 Dihedral : 24.969 156.943 2028 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 11.52 % Favored : 86.91 % 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: 2.86 (0.36), residues: 574 helix: 2.28 (0.28), residues: 336 sheet: 0.30 (0.70), residues: 48 loop : 1.87 (0.51), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 95 HIS 0.003 0.001 HIS A 168 PHE 0.016 0.002 PHE B 22 TYR 0.008 0.001 TYR B 117 ARG 0.003 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 382) hydrogen bonds : angle 3.48171 ( 1017) covalent geometry : bond 0.00300 ( 7488) covalent geometry : angle 0.57289 (10603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.935 Fit side-chains REVERT: A 40 ILE cc_start: 0.6811 (mp) cc_final: 0.6605 (mp) REVERT: A 140 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 162 ASP cc_start: 0.6985 (t0) cc_final: 0.6699 (m-30) REVERT: B 44 ASN cc_start: 0.6347 (t0) cc_final: 0.6061 (t0) REVERT: B 149 ILE cc_start: 0.8225 (mt) cc_final: 0.7786 (mm) REVERT: B 163 LYS cc_start: 0.7768 (tttt) cc_final: 0.7078 (mttm) REVERT: B 173 GLN cc_start: 0.7614 (mt0) cc_final: 0.7262 (mm110) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.3193 time to fit residues: 36.8566 Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.188623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152042 restraints weight = 7293.695| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.27 r_work: 0.3397 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7488 Z= 0.154 Angle : 0.574 9.695 10603 Z= 0.326 Chirality : 0.040 0.215 1184 Planarity : 0.004 0.043 952 Dihedral : 24.951 158.456 2028 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % 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: 2.85 (0.36), residues: 574 helix: 2.34 (0.28), residues: 336 sheet: 0.24 (0.72), residues: 48 loop : 1.75 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 290 HIS 0.003 0.001 HIS A 168 PHE 0.013 0.002 PHE B 22 TYR 0.008 0.001 TYR B 171 ARG 0.002 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 382) hydrogen bonds : angle 3.46101 ( 1017) covalent geometry : bond 0.00331 ( 7488) covalent geometry : angle 0.57394 (10603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.596 Fit side-chains REVERT: A 140 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7445 (p) REVERT: A 167 ASN cc_start: 0.6911 (m-40) cc_final: 0.6223 (m-40) REVERT: B 90 ASP cc_start: 0.6879 (m-30) cc_final: 0.6650 (m-30) REVERT: B 149 ILE cc_start: 0.8298 (mt) cc_final: 0.7877 (mm) REVERT: B 163 LYS cc_start: 0.7709 (tttt) cc_final: 0.7033 (mttp) REVERT: B 173 GLN cc_start: 0.7629 (mt0) cc_final: 0.7281 (mm110) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.3017 time to fit residues: 35.2482 Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.0470 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149801 restraints weight = 7350.142| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.22 r_work: 0.3388 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7488 Z= 0.189 Angle : 0.618 9.560 10603 Z= 0.347 Chirality : 0.042 0.202 1184 Planarity : 0.005 0.042 952 Dihedral : 24.973 158.198 2028 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.95 % Allowed : 13.28 % Favored : 84.77 % 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: 2.53 (0.35), residues: 574 helix: 2.15 (0.28), residues: 336 sheet: 0.16 (0.74), residues: 47 loop : 1.45 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS A 168 PHE 0.011 0.002 PHE B 22 TYR 0.024 0.002 TYR A 289 ARG 0.005 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 382) hydrogen bonds : angle 3.60067 ( 1017) covalent geometry : bond 0.00414 ( 7488) covalent geometry : angle 0.61762 (10603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.613 Fit side-chains REVERT: B 90 ASP cc_start: 0.6977 (m-30) cc_final: 0.6478 (m-30) REVERT: B 149 ILE cc_start: 0.8298 (mt) cc_final: 0.7896 (mm) REVERT: B 163 LYS cc_start: 0.7694 (tttt) cc_final: 0.7030 (mttm) REVERT: B 173 GLN cc_start: 0.7667 (mt0) cc_final: 0.7276 (mm110) REVERT: B 302 SER cc_start: 0.7213 (t) cc_final: 0.6978 (m) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.3493 time to fit residues: 40.0663 Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149794 restraints weight = 7299.532| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.25 r_work: 0.3351 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7488 Z= 0.180 Angle : 0.597 9.688 10603 Z= 0.337 Chirality : 0.041 0.203 1184 Planarity : 0.004 0.037 952 Dihedral : 24.983 158.905 2028 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.37 % Allowed : 13.67 % Favored : 84.96 % 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: 2.50 (0.35), residues: 574 helix: 2.13 (0.28), residues: 336 sheet: 0.15 (0.75), residues: 47 loop : 1.41 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.003 0.001 HIS A 168 PHE 0.013 0.002 PHE B 22 TYR 0.022 0.002 TYR A 289 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 382) hydrogen bonds : angle 3.61642 ( 1017) covalent geometry : bond 0.00392 ( 7488) covalent geometry : angle 0.59738 (10603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.659 Fit side-chains REVERT: A 167 ASN cc_start: 0.6841 (m-40) cc_final: 0.6260 (m110) REVERT: B 90 ASP cc_start: 0.6979 (m-30) cc_final: 0.6467 (m-30) REVERT: B 149 ILE cc_start: 0.8286 (mt) cc_final: 0.7885 (mm) REVERT: B 163 LYS cc_start: 0.7707 (tttt) cc_final: 0.7022 (mttm) REVERT: B 173 GLN cc_start: 0.7686 (mt0) cc_final: 0.7259 (mm110) REVERT: B 302 SER cc_start: 0.7190 (t) cc_final: 0.6964 (m) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.2992 time to fit residues: 32.4557 Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 173 GLN A 177 HIS A 215 ASN B 44 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145735 restraints weight = 7385.270| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.18 r_work: 0.3317 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.006 0.062 7488 Z= 0.291 Angle : 0.723 9.312 10603 Z= 0.401 Chirality : 0.048 0.207 1184 Planarity : 0.006 0.057 952 Dihedral : 25.240 154.954 2028 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.86 % Rotamer: Outliers : 2.54 % Allowed : 13.28 % Favored : 84.18 % 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: 1.81 (0.35), residues: 574 helix: 1.71 (0.28), residues: 334 sheet: 0.02 (0.75), residues: 47 loop : 0.82 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 290 HIS 0.006 0.002 HIS A 236 PHE 0.018 0.003 PHE B 22 TYR 0.019 0.003 TYR A 289 ARG 0.006 0.001 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 382) hydrogen bonds : angle 3.90875 ( 1017) covalent geometry : bond 0.00645 ( 7488) covalent geometry : angle 0.72289 (10603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.560 Fit side-chains REVERT: B 149 ILE cc_start: 0.8423 (mt) cc_final: 0.8144 (mm) REVERT: B 163 LYS cc_start: 0.7700 (tttt) cc_final: 0.6985 (mttm) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.2354 time to fit residues: 24.7071 Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN A 176 GLN B 44 ASN ** B 47 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.187803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152539 restraints weight = 7319.164| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.13 r_work: 0.3400 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7488 Z= 0.143 Angle : 0.578 10.112 10603 Z= 0.326 Chirality : 0.039 0.199 1184 Planarity : 0.004 0.036 952 Dihedral : 25.153 160.198 2028 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 14.84 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.54 (0.36), residues: 574 helix: 2.18 (0.28), residues: 336 sheet: 0.20 (0.75), residues: 46 loop : 1.38 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 PHE 0.009 0.001 PHE B 22 TYR 0.026 0.001 TYR A 289 ARG 0.002 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 382) hydrogen bonds : angle 3.62291 ( 1017) covalent geometry : bond 0.00293 ( 7488) covalent geometry : angle 0.57772 (10603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.600 Fit side-chains REVERT: A 40 ILE cc_start: 0.6835 (mp) cc_final: 0.6623 (mp) REVERT: A 47 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5876 (tp40) REVERT: A 109 LYS cc_start: 0.7096 (tttt) cc_final: 0.6779 (pttt) REVERT: B 90 ASP cc_start: 0.7151 (m-30) cc_final: 0.6576 (m-30) REVERT: B 149 ILE cc_start: 0.8345 (mt) cc_final: 0.7938 (mm) REVERT: B 163 LYS cc_start: 0.7654 (tttt) cc_final: 0.7002 (mttm) REVERT: B 173 GLN cc_start: 0.7652 (mt0) cc_final: 0.7259 (mm110) REVERT: B 223 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6899 (mttp) REVERT: B 259 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7203 (tm-30) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.3010 time to fit residues: 33.5692 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.186979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149450 restraints weight = 7418.150| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.25 r_work: 0.3369 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7488 Z= 0.147 Angle : 0.571 9.904 10603 Z= 0.321 Chirality : 0.039 0.206 1184 Planarity : 0.004 0.038 952 Dihedral : 25.049 157.812 2028 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 14.84 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.36), residues: 574 helix: 2.29 (0.28), residues: 336 sheet: 0.08 (0.76), residues: 47 loop : 1.40 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS A 168 PHE 0.011 0.002 PHE B 22 TYR 0.023 0.002 TYR A 289 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 382) hydrogen bonds : angle 3.59715 ( 1017) covalent geometry : bond 0.00314 ( 7488) covalent geometry : angle 0.57117 (10603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.664 Fit side-chains REVERT: A 47 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5893 (tp40) REVERT: B 90 ASP cc_start: 0.7082 (m-30) cc_final: 0.6494 (m-30) REVERT: B 149 ILE cc_start: 0.8282 (mt) cc_final: 0.7859 (mm) REVERT: B 163 LYS cc_start: 0.7679 (tttt) cc_final: 0.6969 (mttp) REVERT: B 173 GLN cc_start: 0.7674 (mt0) cc_final: 0.7240 (mm110) REVERT: B 259 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7190 (tm-30) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.3124 time to fit residues: 32.6274 Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148181 restraints weight = 7342.277| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.16 r_work: 0.3353 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7488 Z= 0.200 Angle : 0.619 9.671 10603 Z= 0.345 Chirality : 0.042 0.206 1184 Planarity : 0.005 0.041 952 Dihedral : 25.027 155.250 2028 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.56 % Allowed : 15.04 % Favored : 83.40 % 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: 2.44 (0.35), residues: 574 helix: 2.17 (0.28), residues: 336 sheet: -0.02 (0.76), residues: 47 loop : 1.25 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS B 274 PHE 0.014 0.002 PHE B 22 TYR 0.020 0.002 TYR A 289 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 382) hydrogen bonds : angle 3.67882 ( 1017) covalent geometry : bond 0.00441 ( 7488) covalent geometry : angle 0.61886 (10603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.39 seconds wall clock time: 63 minutes 17.90 seconds (3797.90 seconds total)