Starting phenix.real_space_refine on Thu Jul 2 05:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_48616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_48616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_48616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_48616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mty_48616/07_2026/9mty_48616.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.33, per 1000 atoms: 0.19 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: 0.41 Conformation dependent library (CDL) restraints added in 224.8 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: 0.76 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: 0.83 Time building geometry restraints manager: 0.61 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=" C3' DT F 2 " pdb=" O3' DT F 2 " ideal model delta sigma weight residual 1.435 1.369 0.066 1.30e-02 5.92e+03 2.59e+01 bond pdb=" N9 G C 32 " pdb=" C4 G C 32 " ideal model delta sigma weight residual 1.375 1.336 0.039 8.00e-03 1.56e+04 2.40e+01 bond pdb=" C3' DA F 5 " pdb=" O3' DA F 5 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.28e+01 bond pdb=" C5 G C 32 " pdb=" C4 G C 32 " ideal model delta sigma weight residual 1.379 1.346 0.033 7.00e-03 2.04e+04 2.24e+01 bond pdb=" C3' DG E -8 " pdb=" C2' DG E -8 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.11e+01 ... (remaining 7483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9735 2.14 - 4.28: 763 4.28 - 6.42: 96 6.42 - 8.56: 7 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 108.00 117.56 -9.56 7.00e-01 2.04e+00 1.86e+02 angle pdb=" O4' DA D -6 " pdb=" C1' DA D -6 " pdb=" N9 DA D -6 " ideal model delta sigma weight residual 108.00 115.23 -7.23 7.00e-01 2.04e+00 1.07e+02 angle pdb=" O4' DA D -23 " pdb=" C1' DA D -23 " pdb=" N9 DA D -23 " ideal model delta sigma weight residual 108.00 113.97 -5.97 7.00e-01 2.04e+00 7.26e+01 angle pdb=" O5' DG D -5 " pdb=" C5' DG D -5 " pdb=" C4' DG D -5 " ideal model delta sigma weight residual 109.40 115.53 -6.13 8.00e-01 1.56e+00 5.87e+01 angle pdb=" O4' DT G 6 " pdb=" C1' DT G 6 " pdb=" N1 DT G 6 " ideal model delta sigma weight residual 108.00 113.20 -5.20 7.00e-01 2.04e+00 5.53e+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 - 0.079: 836 0.079 - 0.158: 284 0.158 - 0.237: 47 0.237 - 0.316: 11 0.316 - 0.395: 6 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 2.43 2.04 0.39 2.00e-01 2.50e+01 3.89e+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' DA D -6 " pdb=" O4' DA D -6 " pdb=" C2' DA D -6 " pdb=" N9 DA D -6 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.73e+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 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.010 0.090 7488 Z= 0.733 Angle : 1.196 10.705 10603 Z= 0.923 Chirality : 0.082 0.395 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (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 ARG 0.027 0.003 ARG A 130 TYR 0.040 0.008 TYR B 208 PHE 0.030 0.005 PHE A 22 TRP 0.039 0.005 TRP B 321 HIS 0.015 0.004 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.73 ( 7488) covalent geometry : angle 1.19624 / 0.92 (10603) hydrogen bonds : bond 0.11966 / 7.48 ( 382) hydrogen bonds : angle 5.22893 / 3.67 ( 1017) *********************** 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 : 0.199 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: 0.8131 (mt) cc_final: 0.7740 (mm) REVERT: B 163 LYS cc_start: 0.7616 (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: 0.0832 time to fit residues: 13.9677 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4045 r_free = 0.4045 target = 0.185515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148259 restraints weight = 7232.337| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.30 r_work: 0.3354 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7488 Z= 0.182 Angle : 0.737 10.312 10603 Z= 0.437 Chirality : 0.052 0.337 1184 Planarity : 0.006 0.053 952 Dihedral : 24.997 144.235 2028 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.61 % Rotamer: Outliers : 2.54 % Allowed : 6.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.34), residues: 574 helix: 1.08 (0.27), residues: 334 sheet: 0.07 (0.73), residues: 47 loop : 1.47 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 234 TYR 0.017 0.002 TYR A 289 PHE 0.023 0.002 PHE B 22 TRP 0.011 0.002 TRP B 95 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 ( 7488) covalent geometry : angle 0.73739 / 0.44 (10603) hydrogen bonds : bond 0.05245 / 3.33 ( 382) hydrogen bonds : angle 3.93305 / 2.74 ( 1017) *********************** 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 109 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.206 Fit side-chains REVERT: A 152 LYS cc_start: 0.8141 (tttt) cc_final: 0.7676 (mtpt) REVERT: A 162 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: A 167 ASN cc_start: 0.7499 (m110) cc_final: 0.7279 (m-40) REVERT: A 172 THR cc_start: 0.7083 (p) cc_final: 0.6749 (t) REVERT: B 149 ILE cc_start: 0.8215 (mt) cc_final: 0.7806 (mm) REVERT: B 163 LYS cc_start: 0.7843 (tttt) cc_final: 0.7419 (ttmm) outliers start: 13 outliers final: 3 residues processed: 101 average time/residue: 0.0917 time to fit residues: 11.7154 Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 18 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 173 GLN A 177 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** 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 = 0.4009 r_free = 0.4009 target = 0.182225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143410 restraints weight = 7237.754| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.43 r_work: 0.3267 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7488 Z= 0.265 Angle : 0.798 10.353 10603 Z= 0.454 Chirality : 0.055 0.344 1184 Planarity : 0.007 0.072 952 Dihedral : 25.485 142.267 2028 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 9.18 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.35), residues: 574 helix: 1.14 (0.28), residues: 335 sheet: -0.11 (0.71), residues: 47 loop : 1.01 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 221 TYR 0.018 0.003 TYR B 208 PHE 0.017 0.003 PHE B 105 TRP 0.011 0.002 TRP A 290 HIS 0.007 0.002 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 ( 7488) covalent geometry : angle 0.79781 / 0.45 (10603) hydrogen bonds : bond 0.06115 / 3.88 ( 382) hydrogen bonds : angle 4.06513 / 2.84 ( 1017) *********************** 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 90 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.126 Fit side-chains REVERT: A 18 LYS cc_start: 0.6292 (mtpp) cc_final: 0.6049 (mtpp) REVERT: A 152 LYS cc_start: 0.8169 (tttt) cc_final: 0.7745 (mtpt) REVERT: A 162 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: A 172 THR cc_start: 0.6871 (p) cc_final: 0.6500 (t) REVERT: B 149 ILE cc_start: 0.8380 (mt) cc_final: 0.8094 (mm) REVERT: B 163 LYS cc_start: 0.7777 (tttt) cc_final: 0.7029 (mttm) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.0798 time to fit residues: 8.9791 Evaluate side-chains 77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 215 ASN B 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.184099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145244 restraints weight = 7251.444| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7488 Z= 0.195 Angle : 0.704 10.273 10603 Z= 0.405 Chirality : 0.050 0.331 1184 Planarity : 0.005 0.049 952 Dihedral : 25.537 142.011 2028 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 12.70 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.35), residues: 574 helix: 1.45 (0.28), residues: 335 sheet: -0.15 (0.72), residues: 47 loop : 1.11 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.012 0.002 TYR A 289 PHE 0.015 0.002 PHE B 22 TRP 0.009 0.002 TRP B 229 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 ( 7488) covalent geometry : angle 0.70439 / 0.41 (10603) hydrogen bonds : bond 0.04944 / 3.15 ( 382) hydrogen bonds : angle 3.88486 / 2.72 ( 1017) *********************** 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 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.189 Fit side-chains REVERT: A 162 ASP cc_start: 0.7067 (t0) cc_final: 0.6739 (m-30) REVERT: A 172 THR cc_start: 0.6913 (p) cc_final: 0.6583 (t) REVERT: A 268 GLU cc_start: 0.6225 (pm20) cc_final: 0.6002 (pt0) REVERT: B 149 ILE cc_start: 0.8348 (mt) cc_final: 0.8062 (mm) REVERT: B 163 LYS cc_start: 0.7741 (tttt) cc_final: 0.7016 (mttm) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.0914 time to fit residues: 9.4405 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 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 39 ILE Chi-restraints excluded: chain B residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 44 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.183674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144502 restraints weight = 7245.565| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.42 r_work: 0.3284 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7488 Z= 0.209 Angle : 0.704 10.045 10603 Z= 0.402 Chirality : 0.050 0.325 1184 Planarity : 0.005 0.050 952 Dihedral : 25.554 141.113 2028 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 13.28 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.35), residues: 574 helix: 1.53 (0.28), residues: 334 sheet: -0.19 (0.74), residues: 47 loop : 0.89 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 130 TYR 0.011 0.002 TYR B 136 PHE 0.014 0.002 PHE B 22 TRP 0.010 0.002 TRP B 229 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 ( 7488) covalent geometry : angle 0.70431 / 0.40 (10603) hydrogen bonds : bond 0.05096 / 3.24 ( 382) hydrogen bonds : angle 3.89445 / 2.73 ( 1017) *********************** 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 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.219 Fit side-chains REVERT: A 130 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7879 (ttm-80) REVERT: A 172 THR cc_start: 0.6926 (p) cc_final: 0.6595 (t) REVERT: B 149 ILE cc_start: 0.8358 (mt) cc_final: 0.8072 (mm) REVERT: B 163 LYS cc_start: 0.7721 (tttt) cc_final: 0.7020 (mttm) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0952 time to fit residues: 10.3615 Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 157 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4046 r_free = 0.4046 target = 0.185984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147025 restraints weight = 7269.860| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.37 r_work: 0.3313 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7488 Z= 0.157 Angle : 0.629 9.854 10603 Z= 0.363 Chirality : 0.047 0.304 1184 Planarity : 0.005 0.041 952 Dihedral : 25.580 142.682 2028 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.15 % Allowed : 13.87 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.36), residues: 574 helix: 1.84 (0.28), residues: 334 sheet: -0.10 (0.75), residues: 47 loop : 1.10 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.009 0.002 TYR B 124 PHE 0.018 0.002 PHE B 22 TRP 0.009 0.001 TRP A 95 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 7488) covalent geometry : angle 0.62883 / 0.36 (10603) hydrogen bonds : bond 0.04184 / 2.65 ( 382) hydrogen bonds : angle 3.75050 / 2.63 ( 1017) *********************** 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 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.228 Fit side-chains REVERT: A 40 ILE cc_start: 0.6936 (mp) cc_final: 0.6725 (mp) REVERT: A 130 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7926 (ttm-80) REVERT: A 172 THR cc_start: 0.6866 (p) cc_final: 0.6603 (t) REVERT: B 90 ASP cc_start: 0.6968 (m-30) cc_final: 0.6761 (m-30) REVERT: B 149 ILE cc_start: 0.8329 (mt) cc_final: 0.7938 (mm) REVERT: B 163 LYS cc_start: 0.7723 (tttt) cc_final: 0.7031 (mttm) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0895 time to fit residues: 9.6013 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 47 GLN B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.183764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144145 restraints weight = 7263.359| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.43 r_work: 0.3264 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7488 Z= 0.216 Angle : 0.686 9.788 10603 Z= 0.392 Chirality : 0.049 0.314 1184 Planarity : 0.005 0.047 952 Dihedral : 25.592 141.740 2028 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 14.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 574 helix: 1.68 (0.28), residues: 334 sheet: -0.17 (0.75), residues: 47 loop : 0.82 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.010 0.002 TYR B 136 PHE 0.015 0.002 PHE B 22 TRP 0.009 0.002 TRP B 229 HIS 0.005 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 ( 7488) covalent geometry : angle 0.68645 / 0.39 (10603) hydrogen bonds : bond 0.04981 / 3.16 ( 382) hydrogen bonds : angle 3.88579 / 2.73 ( 1017) *********************** 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: 13 poor density : 73 time to evaluate : 0.134 Fit side-chains REVERT: A 130 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: A 172 THR cc_start: 0.6921 (p) cc_final: 0.6617 (t) REVERT: B 90 ASP cc_start: 0.7058 (m-30) cc_final: 0.6837 (m-30) REVERT: B 149 ILE cc_start: 0.8358 (mt) cc_final: 0.8072 (mm) REVERT: B 163 LYS cc_start: 0.7680 (tttt) cc_final: 0.6892 (mtmt) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.0849 time to fit residues: 9.3199 Evaluate side-chains 79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4027 r_free = 0.4027 target = 0.184116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144424 restraints weight = 7295.129| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.40 r_work: 0.3268 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7488 Z= 0.198 Angle : 0.671 9.791 10603 Z= 0.384 Chirality : 0.048 0.313 1184 Planarity : 0.005 0.042 952 Dihedral : 25.590 142.185 2028 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 14.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 574 helix: 1.69 (0.28), residues: 334 sheet: -0.17 (0.75), residues: 47 loop : 0.80 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.009 0.002 TYR B 136 PHE 0.016 0.002 PHE B 22 TRP 0.009 0.002 TRP B 229 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 ( 7488) covalent geometry : angle 0.67075 / 0.38 (10603) hydrogen bonds : bond 0.04728 / 3.01 ( 382) hydrogen bonds : angle 3.89194 / 2.74 ( 1017) *********************** 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 84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.201 Fit side-chains REVERT: A 40 ILE cc_start: 0.6945 (mp) cc_final: 0.6741 (mp) REVERT: A 130 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7867 (ttm-80) REVERT: A 172 THR cc_start: 0.6910 (p) cc_final: 0.6609 (t) REVERT: A 276 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7835 (mmt180) REVERT: B 90 ASP cc_start: 0.7043 (m-30) cc_final: 0.6825 (m-30) REVERT: B 149 ILE cc_start: 0.8347 (mt) cc_final: 0.8057 (mm) REVERT: B 163 LYS cc_start: 0.7694 (tttt) cc_final: 0.6889 (mtmt) outliers start: 13 outliers final: 12 residues processed: 82 average time/residue: 0.0999 time to fit residues: 10.8728 Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4040 r_free = 0.4040 target = 0.185055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148738 restraints weight = 7356.999| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.23 r_work: 0.3345 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7488 Z= 0.157 Angle : 0.613 9.961 10603 Z= 0.354 Chirality : 0.045 0.307 1184 Planarity : 0.004 0.036 952 Dihedral : 25.541 143.628 2028 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.34 % Allowed : 15.04 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.35), residues: 574 helix: 1.87 (0.28), residues: 335 sheet: -0.07 (0.75), residues: 47 loop : 1.12 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.007 0.001 TYR B 124 PHE 0.012 0.002 PHE B 22 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 7488) covalent geometry : angle 0.61301 / 0.35 (10603) hydrogen bonds : bond 0.04048 / 2.56 ( 382) hydrogen bonds : angle 3.78620 / 2.67 ( 1017) *********************** 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 86 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.213 Fit side-chains REVERT: A 40 ILE cc_start: 0.6887 (mp) cc_final: 0.6687 (mp) REVERT: A 130 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7879 (ttm-80) REVERT: A 172 THR cc_start: 0.6783 (p) cc_final: 0.6528 (t) REVERT: A 276 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7721 (mmt180) REVERT: B 90 ASP cc_start: 0.6928 (m-30) cc_final: 0.6676 (m-30) REVERT: B 149 ILE cc_start: 0.8340 (mt) cc_final: 0.8051 (mm) REVERT: B 163 LYS cc_start: 0.7627 (tttt) cc_final: 0.6987 (mttm) REVERT: B 302 SER cc_start: 0.7183 (t) cc_final: 0.6912 (m) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.0915 time to fit residues: 10.0721 Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.186301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149897 restraints weight = 7363.561| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.19 r_work: 0.3367 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7488 Z= 0.134 Angle : 0.592 10.126 10603 Z= 0.343 Chirality : 0.044 0.311 1184 Planarity : 0.004 0.035 952 Dihedral : 25.512 144.222 2028 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 15.43 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.36), residues: 574 helix: 2.02 (0.28), residues: 335 sheet: 0.03 (0.76), residues: 47 loop : 1.30 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.007 0.001 TYR B 124 PHE 0.010 0.002 PHE B 22 TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 7488) covalent geometry : angle 0.59161 / 0.34 (10603) hydrogen bonds : bond 0.03699 / 2.33 ( 382) hydrogen bonds : angle 3.73769 / 2.65 ( 1017) ********************** 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 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.225 Fit side-chains REVERT: A 130 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7908 (ttm-80) REVERT: A 172 THR cc_start: 0.6864 (p) cc_final: 0.6653 (t) REVERT: B 90 ASP cc_start: 0.6844 (m-30) cc_final: 0.6328 (m-30) REVERT: B 149 ILE cc_start: 0.8302 (mt) cc_final: 0.7895 (mm) REVERT: B 163 LYS cc_start: 0.7652 (tttt) cc_final: 0.6984 (mttp) REVERT: B 173 GLN cc_start: 0.7679 (mt0) cc_final: 0.7242 (mm110) REVERT: B 302 SER cc_start: 0.7118 (t) cc_final: 0.6854 (m) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1111 time to fit residues: 11.7014 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 39 ILE 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 2 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN B 47 GLN B 239 ASN 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 = 0.186578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150098 restraints weight = 7371.042| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.17 r_work: 0.3376 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7488 Z= 0.139 Angle : 0.579 10.112 10603 Z= 0.336 Chirality : 0.043 0.316 1184 Planarity : 0.004 0.033 952 Dihedral : 25.437 144.951 2028 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 14.45 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.36), residues: 574 helix: 2.14 (0.28), residues: 335 sheet: 0.07 (0.76), residues: 47 loop : 1.40 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.015 0.001 TYR B 124 PHE 0.011 0.002 PHE B 22 TRP 0.009 0.001 TRP A 95 HIS 0.009 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 ( 7488) covalent geometry : angle 0.57913 / 0.34 (10603) hydrogen bonds : bond 0.03672 / 2.32 ( 382) hydrogen bonds : angle 3.67642 / 2.60 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.29 seconds wall clock time: 24 minutes 12.22 seconds (1452.22 seconds total)