Starting phenix.real_space_refine on Tue Aug 4 21:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mty_48616/08_2026/9mty_48616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mty_48616/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mty_48616/08_2026/9mty_48616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mty_48616/08_2026/9mty_48616.map" model { file = "/net/cci-nas-00/data/ceres_data/9mty_48616/08_2026/9mty_48616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mty_48616/08_2026/9mty_48616.cif" } 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-2.2rc3-6140/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: 1.56, per 1000 atoms: 0.22 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: 0.49 Conformation dependent library (CDL) restraints added in 314.0 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: 0.84 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: 1.13 Time building geometry restraints manager: 0.65 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: 9679 2.14 - 4.28: 817 4.28 - 6.42: 97 6.42 - 8.56: 8 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' G C 2 " pdb=" C5' G C 2 " pdb=" C4' G C 2 " ideal model delta sigma weight residual 109.40 115.95 -6.55 8.00e-01 1.56e+00 6.71e+01 angle pdb=" O4' G C 32 " pdb=" C1' G C 32 " pdb=" N9 G C 32 " ideal model delta sigma weight residual 108.20 114.47 -6.27 8.00e-01 1.56e+00 6.15e+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: 804 0.079 - 0.158: 312 0.158 - 0.237: 49 0.237 - 0.316: 13 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' G C 2 " pdb=" O4' G C 2 " pdb=" C2' G C 2 " pdb=" N9 G C 2 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.95e+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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- 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= 0.747 Angle : 1.219 10.705 10603 Z= 0.963 Chirality : 0.085 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 0.00958 / 0.75 ( 7488) covalent geometry : angle 1.21888 / 0.96 (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 : 0.132 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: 0.7525 (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: 0.0892 time to fit residues: 14.8504 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 : 0.123 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.186017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.148581 restraints weight = 7230.352| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.31 r_work: 0.3345 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1765 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= 0.171 Angle : 0.743 10.387 10603 Z= 0.436 Chirality : 0.052 0.362 1184 Planarity : 0.006 0.054 952 Dihedral : 24.887 144.578 2028 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.61 % Rotamer: Outliers : 2.34 % Allowed : 6.64 % 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: 1.55 (0.34), residues: 574 helix: 1.11 (0.27), residues: 334 sheet: 0.07 (0.73), residues: 47 loop : 1.48 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.018 0.002 TYR A 289 PHE 0.024 0.002 PHE B 22 TRP 0.013 0.002 TRP B 95 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 ( 7488) covalent geometry : angle 0.74334 / 0.44 (10603) hydrogen bonds : bond 0.05226 / 3.33 ( 382) hydrogen bonds : angle 3.92655 / 2.73 ( 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 108 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.157 Fit side-chains REVERT: A 152 LYS cc_start: 0.8141 (tttt) cc_final: 0.7676 (mtpt) REVERT: A 162 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: A 167 ASN cc_start: 0.7496 (m110) cc_final: 0.7279 (m-40) REVERT: A 172 THR cc_start: 0.7083 (p) cc_final: 0.6748 (t) REVERT: B 149 ILE cc_start: 0.8211 (mt) cc_final: 0.7804 (mm) REVERT: B 163 LYS cc_start: 0.7848 (tttt) cc_final: 0.7427 (ttmm) REVERT: B 223 LYS cc_start: 0.7162 (mmtp) cc_final: 0.6961 (mmmt) outliers start: 12 outliers final: 3 residues processed: 101 average time/residue: 0.0939 time to fit residues: 11.9368 Evaluate side-chains 79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 177 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.185298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146495 restraints weight = 7220.164| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.41 r_work: 0.3303 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7488 Z= 0.185 Angle : 0.709 9.937 10603 Z= 0.408 Chirality : 0.051 0.360 1184 Planarity : 0.006 0.058 952 Dihedral : 25.219 143.945 2028 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.56 % Allowed : 9.18 % Favored : 89.26 % 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: 1.91 (0.35), residues: 574 helix: 1.52 (0.28), residues: 335 sheet: -0.14 (0.69), residues: 47 loop : 1.49 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.014 0.002 TYR B 208 PHE 0.021 0.003 PHE B 22 TRP 0.008 0.002 TRP B 290 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 ( 7488) covalent geometry : angle 0.70889 / 0.41 (10603) hydrogen bonds : bond 0.05043 / 3.17 ( 382) hydrogen bonds : angle 3.83329 / 2.67 ( 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 88 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.128 Fit side-chains REVERT: A 152 LYS cc_start: 0.8064 (tttt) cc_final: 0.7714 (mtpt) REVERT: A 162 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: A 172 THR cc_start: 0.7034 (p) cc_final: 0.6813 (t) REVERT: A 223 LYS cc_start: 0.6362 (mttm) cc_final: 0.6150 (mttt) REVERT: B 149 ILE cc_start: 0.8286 (mt) cc_final: 0.7872 (mm) REVERT: B 163 LYS cc_start: 0.7772 (tttt) cc_final: 0.6992 (mttm) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.0946 time to fit residues: 9.9911 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP 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 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 57 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.7206 > 50:) chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.183710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145399 restraints weight = 7244.039| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.41 r_work: 0.3291 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 7488 Z= 0.235 Angle : 0.753 10.125 10603 Z= 0.426 Chirality : 0.053 0.378 1184 Planarity : 0.006 0.060 952 Dihedral : 25.385 142.449 2028 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 11.13 % Favored : 86.52 % 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: -0.16 (0.70), residues: 47 loop : 1.14 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 221 TYR 0.012 0.002 TYR B 136 PHE 0.018 0.003 PHE B 22 TRP 0.010 0.002 TRP B 229 HIS 0.005 0.002 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 7488) covalent geometry : angle 0.75262 / 0.43 (10603) hydrogen bonds : bond 0.05394 / 3.40 ( 382) hydrogen bonds : angle 3.91701 / 2.74 ( 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 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.148 Fit side-chains REVERT: A 172 THR cc_start: 0.6943 (p) cc_final: 0.6640 (t) REVERT: A 223 LYS cc_start: 0.6521 (mttm) cc_final: 0.6258 (mttt) REVERT: A 268 GLU cc_start: 0.6274 (pm20) cc_final: 0.5998 (pt0) REVERT: B 149 ILE cc_start: 0.8358 (mt) cc_final: 0.8075 (mm) REVERT: B 163 LYS cc_start: 0.7724 (tttt) cc_final: 0.7021 (mttm) REVERT: B 223 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6817 (mtpt) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0856 time to fit residues: 9.4048 Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 40.0000 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.184801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147634 restraints weight = 7242.970| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.25 r_work: 0.3341 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7488 Z= 0.194 Angle : 0.696 9.838 10603 Z= 0.393 Chirality : 0.050 0.354 1184 Planarity : 0.005 0.046 952 Dihedral : 25.439 142.133 2028 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 13.09 % 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 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: 1.83 (0.36), residues: 574 helix: 1.63 (0.28), residues: 334 sheet: -0.21 (0.73), residues: 47 loop : 1.10 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 62 TYR 0.010 0.002 TYR B 136 PHE 0.017 0.002 PHE B 22 TRP 0.010 0.002 TRP B 229 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7488) covalent geometry : angle 0.69583 / 0.39 (10603) hydrogen bonds : bond 0.04802 / 3.04 ( 382) hydrogen bonds : angle 3.84124 / 2.69 ( 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 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.132 Fit side-chains REVERT: A 172 THR cc_start: 0.6917 (p) cc_final: 0.6632 (t) REVERT: B 149 ILE cc_start: 0.8333 (mt) cc_final: 0.8057 (mm) REVERT: B 163 LYS cc_start: 0.7724 (tttt) cc_final: 0.7039 (mttm) REVERT: B 223 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6787 (mmmt) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.0880 time to fit residues: 8.8331 Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 B residue 39 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 GLN 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: 9.9990 chunk 64 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 1 optimal weight: 0.0770 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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** B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.185831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148445 restraints weight = 7266.082| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.23 r_work: 0.3348 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7488 Z= 0.162 Angle : 0.659 10.056 10603 Z= 0.375 Chirality : 0.048 0.349 1184 Planarity : 0.005 0.043 952 Dihedral : 25.494 142.578 2028 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.73 % Allowed : 12.11 % Favored : 85.16 % 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: 2.01 (0.36), residues: 574 helix: 1.82 (0.29), residues: 334 sheet: -0.16 (0.74), residues: 47 loop : 1.07 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.008 0.001 TYR B 289 PHE 0.016 0.002 PHE B 22 TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 7488) covalent geometry : angle 0.65892 / 0.38 (10603) hydrogen bonds : bond 0.04405 / 2.79 ( 382) hydrogen bonds : angle 3.78316 / 2.66 ( 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 89 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.127 Fit side-chains REVERT: A 40 ILE cc_start: 0.6925 (mp) cc_final: 0.6725 (mp) REVERT: A 130 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7900 (ttm-80) REVERT: A 172 THR cc_start: 0.7051 (p) cc_final: 0.6798 (t) REVERT: B 47 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7526 (tp40) REVERT: B 90 ASP cc_start: 0.6965 (m-30) cc_final: 0.6716 (m-30) REVERT: B 149 ILE cc_start: 0.8321 (mt) cc_final: 0.8038 (mm) REVERT: B 163 LYS cc_start: 0.7749 (tttt) cc_final: 0.7022 (mttm) REVERT: B 259 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7432 (tm-30) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.0867 time to fit residues: 9.6458 Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 259 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4013 r_free = 0.4013 target = 0.182714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144674 restraints weight = 7280.279| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.30 r_work: 0.3307 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7488 Z= 0.255 Angle : 0.761 9.957 10603 Z= 0.423 Chirality : 0.054 0.356 1184 Planarity : 0.006 0.054 952 Dihedral : 25.570 141.063 2028 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 13.09 % Favored : 84.57 % 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: 1.48 (0.35), residues: 574 helix: 1.51 (0.28), residues: 334 sheet: -0.34 (0.76), residues: 47 loop : 0.60 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.012 0.003 TYR B 136 PHE 0.019 0.003 PHE B 22 TRP 0.011 0.002 TRP A 290 HIS 0.006 0.002 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 ( 7488) covalent geometry : angle 0.76086 / 0.42 (10603) hydrogen bonds : bond 0.05634 / 3.57 ( 382) hydrogen bonds : angle 4.01318 / 2.82 ( 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 88 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.223 Fit side-chains REVERT: A 130 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7865 (ttm-80) REVERT: A 172 THR cc_start: 0.6971 (p) cc_final: 0.6638 (t) REVERT: B 90 ASP cc_start: 0.7123 (m-30) cc_final: 0.6880 (m-30) REVERT: B 149 ILE cc_start: 0.8322 (mt) cc_final: 0.8046 (mm) REVERT: B 163 LYS cc_start: 0.7691 (tttt) cc_final: 0.6887 (mtmt) REVERT: B 259 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7534 (tm-30) outliers start: 12 outliers final: 10 residues processed: 87 average time/residue: 0.0805 time to fit residues: 9.2809 Evaluate side-chains 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain B residue 259 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.184438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148073 restraints weight = 7401.489| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.23 r_work: 0.3339 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7488 Z= 0.161 Angle : 0.643 10.188 10603 Z= 0.367 Chirality : 0.047 0.337 1184 Planarity : 0.005 0.042 952 Dihedral : 25.516 143.188 2028 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.15 % Allowed : 13.67 % 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 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: 1.89 (0.36), residues: 574 helix: 1.79 (0.29), residues: 334 sheet: -0.19 (0.76), residues: 47 loop : 0.88 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.009 0.002 TYR B 124 PHE 0.014 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 0.00303 / 0.16 ( 7488) covalent geometry : angle 0.64324 / 0.37 (10603) hydrogen bonds : bond 0.04296 / 2.72 ( 382) hydrogen bonds : angle 3.82167 / 2.69 ( 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 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.136 Fit side-chains REVERT: A 130 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7915 (ttm-80) REVERT: A 172 THR cc_start: 0.6913 (p) cc_final: 0.6600 (t) REVERT: B 90 ASP cc_start: 0.7010 (m-30) cc_final: 0.6749 (m-30) REVERT: B 149 ILE cc_start: 0.8352 (mt) cc_final: 0.8065 (mm) REVERT: B 163 LYS cc_start: 0.7698 (tttt) cc_final: 0.7010 (mttm) REVERT: B 259 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7524 (tm-30) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.0863 time to fit residues: 9.4461 Evaluate side-chains 84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 259 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.184411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146347 restraints weight = 7371.248| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.25 r_work: 0.3347 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2979 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= 0.168 Angle : 0.641 10.262 10603 Z= 0.364 Chirality : 0.046 0.344 1184 Planarity : 0.005 0.041 952 Dihedral : 25.477 143.185 2028 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.12 % Allowed : 12.70 % 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 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: 1.87 (0.28), residues: 336 sheet: -0.01 (0.77), residues: 47 loop : 1.01 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.008 0.002 TYR B 136 PHE 0.013 0.002 PHE B 22 TRP 0.008 0.001 TRP A 95 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 7488) covalent geometry : angle 0.64149 / 0.36 (10603) hydrogen bonds : bond 0.04300 / 2.70 ( 382) hydrogen bonds : angle 3.77770 / 2.66 ( 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 94 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.130 Fit side-chains REVERT: A 130 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: A 172 THR cc_start: 0.6929 (p) cc_final: 0.6688 (t) REVERT: B 90 ASP cc_start: 0.6913 (m-30) cc_final: 0.6636 (m-30) REVERT: B 149 ILE cc_start: 0.8349 (mt) cc_final: 0.8061 (mm) REVERT: B 163 LYS cc_start: 0.7652 (tttt) cc_final: 0.7004 (mttm) REVERT: B 259 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: B 302 SER cc_start: 0.7183 (t) cc_final: 0.6926 (m) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.0827 time to fit residues: 9.6414 Evaluate side-chains 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.185308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147302 restraints weight = 7382.641| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.34 r_work: 0.3343 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7488 Z= 0.147 Angle : 0.622 10.353 10603 Z= 0.353 Chirality : 0.045 0.343 1184 Planarity : 0.004 0.034 952 Dihedral : 25.457 143.919 2028 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.73 % Allowed : 13.09 % 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 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: 2.21 (0.36), residues: 574 helix: 1.97 (0.29), residues: 335 sheet: 0.06 (0.77), residues: 47 loop : 1.14 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.008 0.001 TYR A 289 PHE 0.012 0.002 PHE A 53 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 0.00274 / 0.15 ( 7488) covalent geometry : angle 0.62241 / 0.35 (10603) hydrogen bonds : bond 0.03973 / 2.50 ( 382) hydrogen bonds : angle 3.73975 / 2.64 ( 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 84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.125 Fit side-chains REVERT: A 130 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7914 (ttm-80) REVERT: A 172 THR cc_start: 0.6907 (p) cc_final: 0.6667 (t) REVERT: B 90 ASP cc_start: 0.6805 (m-30) cc_final: 0.6529 (m-30) REVERT: B 149 ILE cc_start: 0.8305 (mt) cc_final: 0.7901 (mm) REVERT: B 163 LYS cc_start: 0.7681 (tttt) cc_final: 0.7013 (mttm) REVERT: B 259 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 263 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7927 (mm-40) REVERT: B 302 SER cc_start: 0.7205 (t) cc_final: 0.6946 (m) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.0886 time to fit residues: 9.3875 Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144921 restraints weight = 7394.310| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.29 r_work: 0.3311 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7488 Z= 0.219 Angle : 0.693 10.218 10603 Z= 0.387 Chirality : 0.049 0.347 1184 Planarity : 0.005 0.043 952 Dihedral : 25.467 143.660 2028 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.59 % 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: 1.92 (0.35), residues: 574 helix: 1.83 (0.28), residues: 335 sheet: -0.03 (0.77), residues: 47 loop : 0.80 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.018 0.002 TYR B 124 PHE 0.016 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 0.00452 / 0.22 ( 7488) covalent geometry : angle 0.69276 / 0.39 (10603) hydrogen bonds : bond 0.04804 / 3.03 ( 382) hydrogen bonds : angle 3.89136 / 2.74 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.61 seconds wall clock time: 21 minutes 30.94 seconds (1290.94 seconds total)