Starting phenix.real_space_refine on Wed Sep 17 07:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_48616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_48616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_48616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_48616.map" model { file = "/net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_48616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mty_48616/09_2025/9mty_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-2.0-5805/lib/python3.9/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: 2.37, per 1000 atoms: 0.33 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: 0.83 Conformation dependent library (CDL) restraints added in 376.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.11 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: 1.31 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1086 1.32 - 1.44: 2512 1.44 - 1.56: 3660 1.56 - 1.68: 218 1.68 - 1.80: 12 Bond restraints: 7488 Sorted by residual: bond pdb=" CB ILE B 233 " pdb=" CG2 ILE B 233 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" O5' C C 27 " pdb=" C5' C C 27 " ideal model delta sigma weight residual 1.420 1.389 0.031 1.50e-02 4.44e+03 4.20e+00 bond pdb=" CB ARG A 130 " pdb=" CG ARG A 130 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.14e+00 bond pdb=" CB ASN B 239 " pdb=" CG ASN B 239 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" N9 G C 32 " pdb=" C4 G C 32 " ideal model delta sigma weight residual 1.375 1.336 0.039 2.00e-02 2.50e+03 3.85e+00 ... (remaining 7483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9804 2.14 - 4.28: 718 4.28 - 6.42: 73 6.42 - 8.56: 6 8.56 - 10.71: 2 Bond angle restraints: 10603 Sorted by residual: angle pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " pdb=" N9 DG D -5 " ideal model delta sigma weight residual 108.40 117.56 -9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C4' DG D -5 " pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " ideal model delta sigma weight residual 109.70 102.68 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C2' G C 2 " pdb=" C1' G C 2 " pdb=" N9 G C 2 " ideal model delta sigma weight residual 112.00 118.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" C3' A C 18 " pdb=" O3' A C 18 " pdb=" P A C 19 " ideal model delta sigma weight residual 120.20 127.07 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" O4' DA D -6 " pdb=" C1' DA D -6 " pdb=" N9 DA D -6 " ideal model delta sigma weight residual 108.40 115.23 -6.83 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 3868 30.32 - 60.64: 426 60.64 - 90.95: 48 90.95 - 121.27: 2 121.27 - 151.59: 2 Dihedral angle restraints: 4346 sinusoidal: 2624 harmonic: 1722 Sorted by residual: dihedral pdb=" C3' A C 19 " pdb=" C4' A C 19 " pdb=" O4' A C 19 " pdb=" C1' A C 19 " ideal model delta sinusoidal sigma weight residual 20.00 -24.76 44.76 1 8.00e+00 1.56e-02 4.35e+01 dihedral pdb=" O4' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" C2' A C 19 " ideal model delta sinusoidal sigma weight residual -35.00 9.40 -44.40 1 8.00e+00 1.56e-02 4.28e+01 dihedral pdb=" C5' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" O3' A C 19 " ideal model delta sinusoidal sigma weight residual 82.00 124.70 -42.70 1 8.00e+00 1.56e-02 3.98e+01 ... (remaining 4343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 837 0.076 - 0.153: 298 0.153 - 0.229: 33 0.229 - 0.306: 11 0.306 - 0.382: 5 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1' DG D -5 " pdb=" O4' DG D -5 " pdb=" C2' DG D -5 " pdb=" N9 DG D -5 " both_signs ideal model delta sigma weight residual False 2.42 2.04 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' DC F 4 " pdb=" O4' DC F 4 " pdb=" C2' DC F 4 " pdb=" N1 DC F 4 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1181 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 20 " 0.088 2.00e-02 2.50e+03 5.43e-02 6.65e+01 pdb=" N1 C C 20 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C C 20 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C C 20 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C C 20 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C C 20 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C C 20 " 0.067 2.00e-02 2.50e+03 pdb=" C6 C C 20 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D -6 " 0.045 2.00e-02 2.50e+03 2.89e-02 2.30e+01 pdb=" N9 DA D -6 " -0.082 2.00e-02 2.50e+03 pdb=" C8 DA D -6 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA D -6 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA D -6 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA D -6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D -6 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA D -6 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 32 " 0.044 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G C 32 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 32 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G C 32 " -0.019 2.00e-02 2.50e+03 pdb=" C5 G C 32 " -0.028 2.00e-02 2.50e+03 pdb=" C6 G C 32 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G C 32 " 0.061 2.00e-02 2.50e+03 pdb=" N1 G C 32 " -0.023 2.00e-02 2.50e+03 pdb=" C2 G C 32 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 32 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G C 32 " 0.017 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 37 2.62 - 3.19: 5891 3.19 - 3.76: 12147 3.76 - 4.33: 17191 4.33 - 4.90: 25349 Nonbonded interactions: 60615 Sorted by model distance: nonbonded pdb=" OD1 ASP B 11 " pdb="MG MG B 401 " model vdw 2.052 2.170 nonbonded pdb=" OD1 ASP B 123 " pdb="MG MG B 402 " model vdw 2.171 2.170 nonbonded pdb=" OP1 U C 29 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG MG A 401 " model vdw 2.235 2.170 nonbonded pdb=" OD1 ASP A 123 " pdb="MG MG A 402 " model vdw 2.254 2.170 ... (remaining 60610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 303 or resid 318 through 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: 0.650 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: 0.030 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 7488 Z= 0.420 Angle : 1.159 10.705 10603 Z= 0.699 Chirality : 0.078 0.382 1184 Planarity : 0.014 0.137 952 Dihedral : 21.340 151.590 3230 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.39 % Allowed : 4.69 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00908 ( 7488) covalent geometry : angle 1.15908 (10603) hydrogen bonds : bond 0.11966 ( 382) hydrogen bonds : angle 5.22893 ( 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 : 0.220 Fit side-chains REVERT: A 145 GLU cc_start: 0.6966 (tp30) cc_final: 0.6679 (mm-30) REVERT: A 152 LYS cc_start: 0.7882 (tttt) cc_final: 0.7526 (mtmt) REVERT: B 149 ILE cc_start: 0.8130 (mt) cc_final: 0.7740 (mm) REVERT: B 163 LYS cc_start: 0.7615 (tttt) cc_final: 0.7271 (ttmm) REVERT: B 202 VAL cc_start: 0.8466 (t) cc_final: 0.8262 (m) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.1289 time to fit residues: 21.2582 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 : 0.235 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 177 HIS A 272 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149292 restraints weight = 7194.742| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.28 r_work: 0.3365 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1932 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= 0.183 Angle : 0.689 9.539 10603 Z= 0.392 Chirality : 0.045 0.237 1184 Planarity : 0.006 0.049 952 Dihedral : 24.934 151.033 2028 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.61 % Rotamer: Outliers : 2.34 % Allowed : 6.45 % Favored : 91.21 % 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 aren not related in a simple way. whole: 1.82 (0.35), residues: 574 helix: 1.35 (0.27), residues: 335 sheet: 0.11 (0.72), residues: 47 loop : 1.58 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 221 TYR 0.019 0.002 TYR A 289 PHE 0.023 0.002 PHE B 22 TRP 0.012 0.002 TRP B 95 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7488) covalent geometry : angle 0.68949 (10603) hydrogen bonds : bond 0.04519 ( 382) hydrogen bonds : angle 3.80977 ( 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 112 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.234 Fit side-chains REVERT: A 152 LYS cc_start: 0.8059 (tttt) cc_final: 0.7669 (mtpt) REVERT: A 162 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: B 149 ILE cc_start: 0.8216 (mt) cc_final: 0.7798 (mm) REVERT: B 163 LYS cc_start: 0.7811 (tttt) cc_final: 0.6988 (mttm) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.1353 time to fit residues: 17.8970 Evaluate side-chains 88 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.184884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147231 restraints weight = 7267.231| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.35 r_work: 0.3314 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7488 Z= 0.223 Angle : 0.687 9.595 10603 Z= 0.387 Chirality : 0.046 0.246 1184 Planarity : 0.006 0.055 952 Dihedral : 25.129 149.941 2028 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.76 % Allowed : 9.96 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.35), residues: 574 helix: 1.58 (0.28), residues: 335 sheet: -0.04 (0.71), residues: 47 loop : 1.40 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 221 TYR 0.017 0.002 TYR A 289 PHE 0.015 0.002 PHE B 22 TRP 0.010 0.002 TRP A 290 HIS 0.005 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 7488) covalent geometry : angle 0.68729 (10603) hydrogen bonds : bond 0.04687 ( 382) hydrogen bonds : angle 3.77905 ( 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: 9 poor density : 79 time to evaluate : 0.221 Fit side-chains REVERT: A 18 LYS cc_start: 0.6261 (mtpp) cc_final: 0.6037 (mtpp) REVERT: A 152 LYS cc_start: 0.8003 (tttt) cc_final: 0.7704 (mtpt) REVERT: B 149 ILE cc_start: 0.8337 (mt) cc_final: 0.7934 (mm) REVERT: B 163 LYS cc_start: 0.7746 (tttt) cc_final: 0.7041 (mttm) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.1309 time to fit residues: 13.9918 Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 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: 10.0000 chunk 62 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 173 GLN B 44 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.182206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146637 restraints weight = 7394.862| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.21 r_work: 0.3330 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 7488 Z= 0.307 Angle : 0.767 9.521 10603 Z= 0.427 Chirality : 0.049 0.275 1184 Planarity : 0.006 0.071 952 Dihedral : 25.322 147.073 2028 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.15 % Allowed : 12.30 % 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 aren not related in a simple way. whole: 1.45 (0.35), residues: 574 helix: 1.33 (0.28), residues: 334 sheet: -0.14 (0.74), residues: 47 loop : 0.86 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 294 TYR 0.014 0.003 TYR B 136 PHE 0.019 0.003 PHE B 22 TRP 0.013 0.002 TRP B 229 HIS 0.006 0.002 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 7488) covalent geometry : angle 0.76668 (10603) hydrogen bonds : bond 0.05496 ( 382) hydrogen bonds : angle 4.02679 ( 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 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.231 Fit side-chains REVERT: B 90 ASP cc_start: 0.6899 (m-30) cc_final: 0.6635 (m-30) REVERT: B 149 ILE cc_start: 0.8404 (mt) cc_final: 0.8140 (mm) REVERT: B 163 LYS cc_start: 0.7689 (tttt) cc_final: 0.6992 (mttm) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.1158 time to fit residues: 12.2650 Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 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 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: 8.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN B 44 ASN B 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150541 restraints weight = 7323.771| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.12 r_work: 0.3389 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7488 Z= 0.154 Angle : 0.593 10.212 10603 Z= 0.338 Chirality : 0.041 0.212 1184 Planarity : 0.004 0.044 952 Dihedral : 25.256 154.649 2028 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.54 % Allowed : 13.28 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.36), residues: 574 helix: 1.95 (0.28), residues: 336 sheet: 0.19 (0.75), residues: 46 loop : 1.36 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.015 0.001 TYR A 289 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 covalent geometry : bond 0.00328 ( 7488) covalent geometry : angle 0.59284 (10603) hydrogen bonds : bond 0.03672 ( 382) hydrogen bonds : angle 3.69658 ( 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 94 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.236 Fit side-chains REVERT: B 44 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6433 (t0) REVERT: B 90 ASP cc_start: 0.6955 (m-30) cc_final: 0.6747 (m-30) REVERT: B 149 ILE cc_start: 0.8294 (mt) cc_final: 0.7907 (mm) REVERT: B 163 LYS cc_start: 0.7725 (tttt) cc_final: 0.7035 (mttm) REVERT: B 173 GLN cc_start: 0.7590 (mt0) cc_final: 0.7221 (mm110) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.1183 time to fit residues: 13.7501 Evaluate side-chains 79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 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 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: 4.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147031 restraints weight = 7381.013| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.14 r_work: 0.3335 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7488 Z= 0.246 Angle : 0.675 9.849 10603 Z= 0.379 Chirality : 0.045 0.238 1184 Planarity : 0.005 0.048 952 Dihedral : 25.256 152.645 2028 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 13.87 % 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 aren not related in a simple way. whole: 1.94 (0.35), residues: 574 helix: 1.80 (0.28), residues: 334 sheet: -0.11 (0.77), residues: 47 loop : 0.94 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.019 0.002 TYR A 289 PHE 0.014 0.002 PHE B 105 TRP 0.010 0.002 TRP B 229 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 7488) covalent geometry : angle 0.67497 (10603) hydrogen bonds : bond 0.04646 ( 382) hydrogen bonds : angle 3.84605 ( 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: 13 poor density : 74 time to evaluate : 0.233 Fit side-chains REVERT: A 130 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7934 (ttm-80) REVERT: A 276 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7972 (mtt180) REVERT: B 90 ASP cc_start: 0.7040 (m-30) cc_final: 0.6839 (m-30) REVERT: B 149 ILE cc_start: 0.8348 (mt) cc_final: 0.8065 (mm) REVERT: B 163 LYS cc_start: 0.7719 (tttt) cc_final: 0.7030 (mttm) REVERT: B 173 GLN cc_start: 0.7615 (mt0) cc_final: 0.7250 (mm110) REVERT: B 302 SER cc_start: 0.7204 (t) cc_final: 0.6955 (m) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.1120 time to fit residues: 12.2405 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 : 0.229 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 0.0030 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 45 optimal weight: 7.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN B 44 ASN B 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151539 restraints weight = 7345.828| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.25 r_work: 0.3370 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7488 Z= 0.144 Angle : 0.567 10.264 10603 Z= 0.321 Chirality : 0.040 0.208 1184 Planarity : 0.004 0.039 952 Dihedral : 25.192 159.494 2028 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.34 % Allowed : 13.87 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.36), residues: 574 helix: 2.19 (0.29), residues: 335 sheet: 0.04 (0.76), residues: 49 loop : 1.41 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.022 0.001 TYR A 289 PHE 0.010 0.001 PHE B 22 TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7488) covalent geometry : angle 0.56655 (10603) hydrogen bonds : bond 0.03372 ( 382) hydrogen bonds : angle 3.68211 ( 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 92 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.231 Fit side-chains REVERT: A 40 ILE cc_start: 0.6822 (mp) cc_final: 0.6619 (mp) REVERT: A 276 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7843 (mtt180) REVERT: B 90 ASP cc_start: 0.6898 (m-30) cc_final: 0.6390 (m-30) REVERT: B 149 ILE cc_start: 0.8266 (mt) cc_final: 0.7840 (mm) REVERT: B 163 LYS cc_start: 0.7696 (tttt) cc_final: 0.6953 (mttp) REVERT: B 173 GLN cc_start: 0.7684 (mt0) cc_final: 0.7262 (mm110) REVERT: B 223 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6943 (mmtp) REVERT: B 302 SER cc_start: 0.7041 (t) cc_final: 0.6799 (m) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.1182 time to fit residues: 13.4111 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 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 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 215 ASN B 47 GLN B 167 ASN 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 = 0.182130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.146159 restraints weight = 7431.052| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.15 r_work: 0.3320 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7488 Z= 0.287 Angle : 0.713 9.792 10603 Z= 0.396 Chirality : 0.047 0.223 1184 Planarity : 0.006 0.051 952 Dihedral : 25.295 153.979 2028 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.73 % Allowed : 14.26 % 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 aren not related in a simple way. whole: 1.93 (0.36), residues: 574 helix: 1.80 (0.28), residues: 334 sheet: -0.08 (0.77), residues: 47 loop : 0.92 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 294 TYR 0.016 0.003 TYR A 289 PHE 0.017 0.003 PHE B 22 TRP 0.012 0.002 TRP B 229 HIS 0.007 0.002 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 7488) covalent geometry : angle 0.71324 (10603) hydrogen bonds : bond 0.05069 ( 382) hydrogen bonds : angle 4.01225 ( 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: 14 poor density : 73 time to evaluate : 0.250 Fit side-chains REVERT: A 130 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7713 (ttm-80) REVERT: B 149 ILE cc_start: 0.8367 (mt) cc_final: 0.8077 (mm) REVERT: B 163 LYS cc_start: 0.7643 (tttt) cc_final: 0.6882 (mtmt) REVERT: B 173 GLN cc_start: 0.7716 (mt0) cc_final: 0.7283 (mm110) REVERT: B 302 SER cc_start: 0.7258 (t) cc_final: 0.7000 (m) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.1226 time to fit residues: 12.9680 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 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 A residue 215 ASN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 GLN 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: 5.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 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 = 0.4041 r_free = 0.4041 target = 0.185230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149456 restraints weight = 7378.452| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.15 r_work: 0.3363 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7488 Z= 0.159 Angle : 0.599 10.155 10603 Z= 0.338 Chirality : 0.041 0.207 1184 Planarity : 0.006 0.129 952 Dihedral : 25.245 157.545 2028 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 15.82 % Favored : 82.23 % 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 aren not related in a simple way. whole: 2.39 (0.36), residues: 574 helix: 2.08 (0.29), residues: 335 sheet: 0.00 (0.77), residues: 47 loop : 1.32 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.022 0.002 TYR A 289 PHE 0.013 0.002 PHE B 22 TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7488) covalent geometry : angle 0.59892 (10603) hydrogen bonds : bond 0.03703 ( 382) hydrogen bonds : angle 3.79151 ( 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 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.242 Fit side-chains REVERT: A 130 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: B 90 ASP cc_start: 0.7212 (m-30) cc_final: 0.6610 (m-30) REVERT: B 149 ILE cc_start: 0.8322 (mt) cc_final: 0.7917 (mm) REVERT: B 163 LYS cc_start: 0.7652 (tttt) cc_final: 0.6985 (mttp) REVERT: B 173 GLN cc_start: 0.7683 (mt0) cc_final: 0.7325 (mm110) REVERT: B 302 SER cc_start: 0.7170 (t) cc_final: 0.6917 (m) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1232 time to fit residues: 12.8445 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN 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 = 0.4059 r_free = 0.4059 target = 0.187080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151355 restraints weight = 7374.672| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.16 r_work: 0.3387 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7488 Z= 0.143 Angle : 0.572 10.186 10603 Z= 0.323 Chirality : 0.039 0.207 1184 Planarity : 0.006 0.121 952 Dihedral : 25.110 158.504 2028 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 15.43 % Favored : 82.03 % 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 aren not related in a simple way. whole: 2.60 (0.36), residues: 574 helix: 2.26 (0.29), residues: 335 sheet: 0.05 (0.77), residues: 49 loop : 1.43 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.021 0.001 TYR A 289 PHE 0.010 0.001 PHE B 22 TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7488) covalent geometry : angle 0.57223 (10603) hydrogen bonds : bond 0.03345 ( 382) hydrogen bonds : angle 3.71837 ( 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 92 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.237 Fit side-chains REVERT: A 59 LYS cc_start: 0.6253 (mtmt) cc_final: 0.5782 (mmtm) REVERT: A 130 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7768 (ttm-80) REVERT: B 90 ASP cc_start: 0.7193 (m-30) cc_final: 0.6596 (m-30) REVERT: B 149 ILE cc_start: 0.8295 (mt) cc_final: 0.7871 (mm) REVERT: B 163 LYS cc_start: 0.7582 (tttt) cc_final: 0.6977 (mttp) REVERT: B 173 GLN cc_start: 0.7651 (mt0) cc_final: 0.7329 (mm110) REVERT: B 302 SER cc_start: 0.7073 (t) cc_final: 0.6834 (m) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.1234 time to fit residues: 13.8429 Evaluate side-chains 86 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 130 ARG 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 2 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150884 restraints weight = 7384.907| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.16 r_work: 0.3397 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 7488 Z= 0.248 Angle : 1.053 59.197 10603 Z= 0.633 Chirality : 0.040 0.204 1184 Planarity : 0.007 0.142 952 Dihedral : 25.106 158.476 2028 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.15 % Allowed : 15.23 % Favored : 82.62 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: 2.56 (0.36), residues: 574 helix: 2.26 (0.29), residues: 335 sheet: 0.06 (0.77), residues: 49 loop : 1.33 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.019 0.002 TYR A 289 PHE 0.009 0.002 PHE B 22 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 7488) covalent geometry : angle 1.05267 (10603) hydrogen bonds : bond 0.03383 ( 382) hydrogen bonds : angle 3.72070 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.82 seconds wall clock time: 29 minutes 49.16 seconds (1789.16 seconds total)