Starting phenix.real_space_refine on Sat May 10 20:48:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mty_48616/05_2025/9mty_48616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mty_48616/05_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_48616/05_2025/9mty_48616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mty_48616/05_2025/9mty_48616.map" model { file = "/net/cci-nas-00/data/ceres_data/9mty_48616/05_2025/9mty_48616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mty_48616/05_2025/9mty_48616.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 111 5.49 5 Mg 4 5.21 5 S 8 5.16 5 C 4140 2.51 5 N 1279 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7106 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2384 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2401 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 2 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 759 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 10, 'rna3p': 25} Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.30, per 1000 atoms: 0.75 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: 2.24 Conformation dependent library (CDL) restraints added in 628.4 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 64.8% alpha, 5.3% beta 41 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.947A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 removed outlier: 4.163A pdb=" N SER A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 165 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.742A pdb=" N PHE A 199 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 230 through 248 removed outlier: 4.090A pdb=" N ARG A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.718A pdb=" N GLU A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.662A pdb=" N ALA A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 66 through 72 Processing helix chain 'B' and resid 73 through 74 No H-bonds generated for 'chain 'B' and resid 73 through 74' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 112 through 138 removed outlier: 3.980A pdb=" N SER B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 165 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.885A pdb=" N ARG B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.506A pdb=" N GLU B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 269 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AA3, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.621A pdb=" N ALA B 20 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 40 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 213 through 214 280 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1086 1.32 - 1.44: 2512 1.44 - 1.56: 3660 1.56 - 1.68: 218 1.68 - 1.80: 12 Bond restraints: 7488 Sorted by residual: bond pdb=" CB ILE B 233 " pdb=" CG2 ILE B 233 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" O5' C C 27 " pdb=" C5' C C 27 " ideal model delta sigma weight residual 1.420 1.389 0.031 1.50e-02 4.44e+03 4.20e+00 bond pdb=" CB ARG A 130 " pdb=" CG ARG A 130 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.14e+00 bond pdb=" CB ASN B 239 " pdb=" CG ASN B 239 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" N9 G C 32 " pdb=" C4 G C 32 " ideal model delta sigma weight residual 1.375 1.336 0.039 2.00e-02 2.50e+03 3.85e+00 ... (remaining 7483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9804 2.14 - 4.28: 718 4.28 - 6.42: 73 6.42 - 8.56: 6 8.56 - 10.71: 2 Bond angle restraints: 10603 Sorted by residual: angle pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " pdb=" N9 DG D -5 " ideal model delta sigma weight residual 108.40 117.56 -9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C4' DG D -5 " pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " ideal model delta sigma weight residual 109.70 102.68 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C2' G C 2 " pdb=" C1' G C 2 " pdb=" N9 G C 2 " ideal model delta sigma weight residual 112.00 118.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" C3' A C 18 " pdb=" O3' A C 18 " pdb=" P A C 19 " ideal model delta sigma weight residual 120.20 127.07 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" O4' DA D -6 " pdb=" C1' DA D -6 " pdb=" N9 DA D -6 " ideal model delta sigma weight residual 108.40 115.23 -6.83 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 3868 30.32 - 60.64: 426 60.64 - 90.95: 48 90.95 - 121.27: 2 121.27 - 151.59: 2 Dihedral angle restraints: 4346 sinusoidal: 2624 harmonic: 1722 Sorted by residual: dihedral pdb=" C3' A C 19 " pdb=" C4' A C 19 " pdb=" O4' A C 19 " pdb=" C1' A C 19 " ideal model delta sinusoidal sigma weight residual 20.00 -24.76 44.76 1 8.00e+00 1.56e-02 4.35e+01 dihedral pdb=" O4' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" C2' A C 19 " ideal model delta sinusoidal sigma weight residual -35.00 9.40 -44.40 1 8.00e+00 1.56e-02 4.28e+01 dihedral pdb=" C5' A C 19 " pdb=" C4' A C 19 " pdb=" C3' A C 19 " pdb=" O3' A C 19 " ideal model delta sinusoidal sigma weight residual 82.00 124.70 -42.70 1 8.00e+00 1.56e-02 3.98e+01 ... (remaining 4343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 837 0.076 - 0.153: 298 0.153 - 0.229: 33 0.229 - 0.306: 11 0.306 - 0.382: 5 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1' DG D -5 " pdb=" O4' DG D -5 " pdb=" C2' DG D -5 " pdb=" N9 DG D -5 " both_signs ideal model delta sigma weight residual False 2.42 2.04 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' DC F 4 " pdb=" O4' DC F 4 " pdb=" C2' DC F 4 " pdb=" N1 DC F 4 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1181 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 20 " 0.088 2.00e-02 2.50e+03 5.43e-02 6.65e+01 pdb=" N1 C C 20 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C C 20 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C C 20 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C C 20 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C C 20 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C C 20 " 0.067 2.00e-02 2.50e+03 pdb=" C6 C C 20 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D -6 " 0.045 2.00e-02 2.50e+03 2.89e-02 2.30e+01 pdb=" N9 DA D -6 " -0.082 2.00e-02 2.50e+03 pdb=" C8 DA D -6 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA D -6 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA D -6 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA D -6 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA D -6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D -6 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA D -6 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 32 " 0.044 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G C 32 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 32 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G C 32 " -0.019 2.00e-02 2.50e+03 pdb=" C5 G C 32 " -0.028 2.00e-02 2.50e+03 pdb=" C6 G C 32 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G C 32 " 0.061 2.00e-02 2.50e+03 pdb=" N1 G C 32 " -0.023 2.00e-02 2.50e+03 pdb=" C2 G C 32 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 32 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G C 32 " 0.017 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 37 2.62 - 3.19: 5891 3.19 - 3.76: 12147 3.76 - 4.33: 17191 4.33 - 4.90: 25349 Nonbonded interactions: 60615 Sorted by model distance: nonbonded pdb=" OD1 ASP B 11 " pdb="MG MG B 401 " model vdw 2.052 2.170 nonbonded pdb=" OD1 ASP B 123 " pdb="MG MG B 402 " model vdw 2.171 2.170 nonbonded pdb=" OP1 U C 29 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG MG A 401 " model vdw 2.235 2.170 nonbonded pdb=" OD1 ASP A 123 " pdb="MG MG A 402 " model vdw 2.254 2.170 ... (remaining 60610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 303 or resid 318 through 322 or resid 401 throug \ h 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.240 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 7488 Z= 0.420 Angle : 1.159 10.705 10603 Z= 0.699 Chirality : 0.078 0.382 1184 Planarity : 0.014 0.137 952 Dihedral : 21.340 151.590 3230 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.39 % Allowed : 4.69 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.32), residues: 574 helix: -0.79 (0.22), residues: 333 sheet: -0.08 (0.74), residues: 46 loop : 1.09 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 321 HIS 0.015 0.004 HIS B 320 PHE 0.030 0.005 PHE A 22 TYR 0.040 0.008 TYR B 208 ARG 0.027 0.003 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.11966 ( 382) hydrogen bonds : angle 5.22893 ( 1017) covalent geometry : bond 0.00908 ( 7488) covalent geometry : angle 1.15908 (10603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.624 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: 0.2490 time to fit residues: 41.0174 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 : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 272 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.186712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150207 restraints weight = 7140.701| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.20 r_work: 0.3371 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7488 Z= 0.185 Angle : 0.696 9.698 10603 Z= 0.397 Chirality : 0.045 0.252 1184 Planarity : 0.006 0.050 952 Dihedral : 24.863 150.487 2028 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.39 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 7.03 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 574 helix: 1.27 (0.27), residues: 335 sheet: 0.09 (0.72), residues: 47 loop : 1.56 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 95 HIS 0.006 0.001 HIS A 168 PHE 0.024 0.002 PHE B 22 TYR 0.020 0.002 TYR A 289 ARG 0.005 0.001 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 382) hydrogen bonds : angle 3.84591 ( 1017) covalent geometry : bond 0.00398 ( 7488) covalent geometry : angle 0.69580 (10603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.607 Fit side-chains REVERT: A 152 LYS cc_start: 0.8104 (tttt) cc_final: 0.7663 (mtpt) REVERT: A 162 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: A 172 THR cc_start: 0.7185 (p) cc_final: 0.6969 (t) REVERT: B 149 ILE cc_start: 0.8208 (mt) cc_final: 0.7795 (mm) REVERT: B 163 LYS cc_start: 0.7818 (tttt) cc_final: 0.7409 (ttmm) outliers start: 10 outliers final: 3 residues processed: 105 average time/residue: 0.2732 time to fit residues: 35.5047 Evaluate side-chains 85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.187669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150319 restraints weight = 7410.553| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.34 r_work: 0.3366 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7488 Z= 0.172 Angle : 0.622 9.686 10603 Z= 0.354 Chirality : 0.042 0.221 1184 Planarity : 0.005 0.045 952 Dihedral : 25.061 152.773 2028 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.56 % Allowed : 8.79 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.36), residues: 574 helix: 1.89 (0.28), residues: 336 sheet: 0.03 (0.70), residues: 47 loop : 1.65 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS B 288 PHE 0.017 0.002 PHE B 22 TYR 0.010 0.002 TYR B 117 ARG 0.004 0.000 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 382) hydrogen bonds : angle 3.60891 ( 1017) covalent geometry : bond 0.00369 ( 7488) covalent geometry : angle 0.62190 (10603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.614 Fit side-chains REVERT: A 18 LYS cc_start: 0.6317 (mtpp) cc_final: 0.6106 (mtpp) REVERT: A 140 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7309 (p) REVERT: A 152 LYS cc_start: 0.7842 (tttt) cc_final: 0.7559 (mtpt) REVERT: A 162 ASP cc_start: 0.7063 (t0) cc_final: 0.6770 (m-30) REVERT: A 172 THR cc_start: 0.6981 (p) cc_final: 0.6777 (t) REVERT: B 149 ILE cc_start: 0.8283 (mt) cc_final: 0.7849 (mm) REVERT: B 163 LYS cc_start: 0.7747 (tttt) cc_final: 0.7066 (mttm) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.2719 time to fit residues: 32.3921 Evaluate side-chains 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 1 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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** 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 = 0.186445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149899 restraints weight = 7400.845| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.17 r_work: 0.3387 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7488 Z= 0.183 Angle : 0.626 9.651 10603 Z= 0.355 Chirality : 0.042 0.227 1184 Planarity : 0.005 0.050 952 Dihedral : 25.086 154.474 2028 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.76 % Allowed : 10.74 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.36), residues: 574 helix: 1.97 (0.28), residues: 335 sheet: 0.13 (0.71), residues: 47 loop : 1.56 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 168 PHE 0.011 0.002 PHE B 147 TYR 0.009 0.002 TYR B 117 ARG 0.002 0.000 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 382) hydrogen bonds : angle 3.62731 ( 1017) covalent geometry : bond 0.00400 ( 7488) covalent geometry : angle 0.62583 (10603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.640 Fit side-chains REVERT: A 140 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7382 (p) REVERT: B 90 ASP cc_start: 0.6745 (m-30) cc_final: 0.6514 (m-30) REVERT: B 149 ILE cc_start: 0.8282 (mt) cc_final: 0.7882 (mm) REVERT: B 163 LYS cc_start: 0.7732 (tttt) cc_final: 0.7040 (mttm) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.2713 time to fit residues: 30.5234 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.186908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.149031 restraints weight = 7297.991| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.35 r_work: 0.3368 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7488 Z= 0.173 Angle : 0.608 9.756 10603 Z= 0.345 Chirality : 0.042 0.223 1184 Planarity : 0.005 0.043 952 Dihedral : 25.042 157.865 2028 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.36), residues: 574 helix: 2.03 (0.28), residues: 336 sheet: 0.09 (0.73), residues: 47 loop : 1.55 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.003 0.001 HIS A 168 PHE 0.014 0.002 PHE B 22 TYR 0.008 0.002 TYR B 289 ARG 0.004 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 382) hydrogen bonds : angle 3.61920 ( 1017) covalent geometry : bond 0.00379 ( 7488) covalent geometry : angle 0.60789 (10603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.683 Fit side-chains REVERT: B 90 ASP cc_start: 0.6864 (m-30) cc_final: 0.6641 (m-30) REVERT: B 149 ILE cc_start: 0.8299 (mt) cc_final: 0.7902 (mm) REVERT: B 163 LYS cc_start: 0.7711 (tttt) cc_final: 0.7048 (mttm) REVERT: B 173 GLN cc_start: 0.7693 (mt0) cc_final: 0.7311 (mm110) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.2537 time to fit residues: 27.9854 Evaluate side-chains 79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.185424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147544 restraints weight = 7310.569| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.26 r_work: 0.3360 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7488 Z= 0.173 Angle : 0.597 9.799 10603 Z= 0.339 Chirality : 0.041 0.208 1184 Planarity : 0.004 0.038 952 Dihedral : 25.036 159.836 2028 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.36), residues: 574 helix: 2.04 (0.28), residues: 336 sheet: 0.12 (0.75), residues: 47 loop : 1.41 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS A 168 PHE 0.011 0.002 PHE B 53 TYR 0.026 0.002 TYR A 289 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 382) hydrogen bonds : angle 3.63256 ( 1017) covalent geometry : bond 0.00376 ( 7488) covalent geometry : angle 0.59685 (10603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.635 Fit side-chains REVERT: A 59 LYS cc_start: 0.6187 (mtmt) cc_final: 0.5650 (mmtm) REVERT: B 90 ASP cc_start: 0.7027 (m-30) cc_final: 0.6532 (m-30) REVERT: B 149 ILE cc_start: 0.8249 (mt) cc_final: 0.7836 (mm) REVERT: B 163 LYS cc_start: 0.7700 (tttt) cc_final: 0.6960 (mttp) REVERT: B 173 GLN cc_start: 0.7698 (mt0) cc_final: 0.7257 (mm110) REVERT: B 302 SER cc_start: 0.7186 (t) cc_final: 0.6956 (m) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.2515 time to fit residues: 28.3482 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 : 0.637 ------------------------------------------------------------------------------- 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 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.182625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146415 restraints weight = 7301.336| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.23 r_work: 0.3326 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7488 Z= 0.248 Angle : 0.681 9.525 10603 Z= 0.379 Chirality : 0.045 0.210 1184 Planarity : 0.005 0.047 952 Dihedral : 25.228 157.865 2028 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.54 % Allowed : 13.09 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.35), residues: 574 helix: 1.77 (0.28), residues: 334 sheet: 0.02 (0.76), residues: 47 loop : 0.98 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 229 HIS 0.005 0.001 HIS A 236 PHE 0.016 0.002 PHE B 22 TYR 0.019 0.002 TYR A 289 ARG 0.005 0.001 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 382) hydrogen bonds : angle 3.84616 ( 1017) covalent geometry : bond 0.00547 ( 7488) covalent geometry : angle 0.68144 (10603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.674 Fit side-chains REVERT: B 149 ILE cc_start: 0.8355 (mt) cc_final: 0.8069 (mm) REVERT: B 163 LYS cc_start: 0.7715 (tttt) cc_final: 0.6872 (mttp) REVERT: B 302 SER cc_start: 0.7240 (t) cc_final: 0.6997 (m) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.2448 time to fit residues: 26.0573 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 : 0.601 ------------------------------------------------------------------------------- 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 44 ASN Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- 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 44 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 = 0.4066 r_free = 0.4066 target = 0.187392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149961 restraints weight = 7298.799| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.25 r_work: 0.3384 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3124 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= 0.139 Angle : 0.565 10.157 10603 Z= 0.319 Chirality : 0.039 0.198 1184 Planarity : 0.004 0.038 952 Dihedral : 25.144 162.302 2028 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.76 % Allowed : 14.06 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.36), residues: 574 helix: 2.16 (0.28), residues: 336 sheet: 0.13 (0.75), residues: 47 loop : 1.44 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS B 168 PHE 0.011 0.002 PHE B 22 TYR 0.024 0.001 TYR A 289 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 382) hydrogen bonds : angle 3.60955 ( 1017) covalent geometry : bond 0.00294 ( 7488) covalent geometry : angle 0.56535 (10603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.588 Fit side-chains REVERT: B 90 ASP cc_start: 0.7161 (m-30) cc_final: 0.6579 (m-30) REVERT: B 144 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6795 (mm-30) REVERT: B 149 ILE cc_start: 0.8256 (mt) cc_final: 0.7839 (mm) REVERT: B 163 LYS cc_start: 0.7679 (tttt) cc_final: 0.6957 (mttp) REVERT: B 173 GLN cc_start: 0.7665 (mt0) cc_final: 0.7286 (mm110) REVERT: B 223 LYS cc_start: 0.7277 (mmmt) cc_final: 0.6922 (mttp) REVERT: B 302 SER cc_start: 0.7090 (t) cc_final: 0.6872 (m) outliers start: 9 outliers final: 9 residues processed: 90 average time/residue: 0.2322 time to fit residues: 26.7055 Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain B residue 10 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.188141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150590 restraints weight = 7343.601| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.27 r_work: 0.3394 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3224 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= 0.136 Angle : 0.560 10.059 10603 Z= 0.315 Chirality : 0.039 0.207 1184 Planarity : 0.004 0.044 952 Dihedral : 25.056 160.718 2028 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 14.84 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.36), residues: 574 helix: 2.28 (0.28), residues: 336 sheet: 0.17 (0.76), residues: 47 loop : 1.56 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 168 PHE 0.010 0.001 PHE B 22 TYR 0.025 0.001 TYR A 289 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 382) hydrogen bonds : angle 3.59493 ( 1017) covalent geometry : bond 0.00289 ( 7488) covalent geometry : angle 0.55952 (10603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.643 Fit side-chains REVERT: A 47 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5901 (tp40) REVERT: A 59 LYS cc_start: 0.6184 (mtmt) cc_final: 0.5701 (mmtm) REVERT: A 109 LYS cc_start: 0.6909 (ptmt) cc_final: 0.6407 (ptmt) REVERT: B 90 ASP cc_start: 0.7070 (m-30) cc_final: 0.6487 (m-30) REVERT: B 144 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6781 (mm-30) REVERT: B 149 ILE cc_start: 0.8261 (mt) cc_final: 0.7839 (mm) REVERT: B 163 LYS cc_start: 0.7687 (tttt) cc_final: 0.6967 (mttp) REVERT: B 173 GLN cc_start: 0.7639 (mt0) cc_final: 0.7282 (mm110) REVERT: B 302 SER cc_start: 0.7070 (t) cc_final: 0.6851 (m) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.2334 time to fit residues: 25.6377 Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 ILE 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 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 173 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.186898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149400 restraints weight = 7469.475| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.27 r_work: 0.3380 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7488 Z= 0.153 Angle : 0.570 9.990 10603 Z= 0.320 Chirality : 0.039 0.207 1184 Planarity : 0.004 0.037 952 Dihedral : 24.993 159.348 2028 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 14.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.36), residues: 574 helix: 2.30 (0.28), residues: 336 sheet: 0.15 (0.76), residues: 47 loop : 1.54 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 95 HIS 0.004 0.001 HIS A 168 PHE 0.011 0.002 PHE B 22 TYR 0.023 0.001 TYR A 289 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 382) hydrogen bonds : angle 3.60032 ( 1017) covalent geometry : bond 0.00329 ( 7488) covalent geometry : angle 0.57040 (10603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.651 Fit side-chains REVERT: A 59 LYS cc_start: 0.6129 (mtmt) cc_final: 0.5603 (mmtm) REVERT: A 109 LYS cc_start: 0.6954 (ptmt) cc_final: 0.6648 (ptmt) REVERT: B 90 ASP cc_start: 0.7099 (m-30) cc_final: 0.6517 (m-30) REVERT: B 144 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6799 (mm-30) REVERT: B 149 ILE cc_start: 0.8279 (mt) cc_final: 0.7864 (mm) REVERT: B 163 LYS cc_start: 0.7649 (tttt) cc_final: 0.6960 (mttp) REVERT: B 173 GLN cc_start: 0.7674 (mt0) cc_final: 0.7304 (mm110) REVERT: B 302 SER cc_start: 0.7116 (t) cc_final: 0.6889 (m) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.2416 time to fit residues: 24.7355 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 : 0.606 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.184719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148244 restraints weight = 7364.504| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.15 r_work: 0.3360 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7488 Z= 0.204 Angle : 0.622 9.835 10603 Z= 0.345 Chirality : 0.042 0.207 1184 Planarity : 0.005 0.041 952 Dihedral : 25.003 157.066 2028 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 14.45 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.36), residues: 574 helix: 2.14 (0.28), residues: 336 sheet: 0.06 (0.75), residues: 47 loop : 1.36 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.004 0.001 HIS A 168 PHE 0.014 0.002 PHE B 22 TYR 0.020 0.002 TYR A 289 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 382) hydrogen bonds : angle 3.68779 ( 1017) covalent geometry : bond 0.00449 ( 7488) covalent geometry : angle 0.62202 (10603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.93 seconds wall clock time: 56 minutes 14.36 seconds (3374.36 seconds total)